Modules

Input

010

Output

singles_truncated discarded paired_truncated collapsed collapsed_truncated paired_interleaved settings versions

adapterremovalfixprefix

adapterremoval fastq dedup

Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.

Input

01

fasta virulence Staphylococcus aureus

Rapid identification of Staphylococcus aureus agr locus type and agr operon variants

Input

01

Output

summary results_dir versions

ale

reference-independent assembly evaluation

ALE: assembly likelihood estimator.

Input

012

Output

ale versions

allelecounter

allele count coverage

Generates a count of coverage of alleles

Input

01200

ampir amp antimicrobial peptide prediction

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

Input

01000

Output

amps_faa amps_tsv versions

amplify_predict

antimicrobial peptides AMPs prediction model

AMPlify is an attentive deep learning model for antimicrobial peptide prediction.

Input

010

Output

tsv versions

Tools

amr antimicrobial resistance arg antimicrobial resistance genes genomics metagenomics normalization drug categorization

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

Input

0100

bam copy number cram

copy number profiles of tumour cells.

Input

01234000000

Output

allelefreqs bafs cnvs logrs metrics png purityploidy segments versions

ashlar

image_processing alignment registration

Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

Input

0100

background cycif autofluorescence image_analysis mcmicro highly_multiplexed_imaging

Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched tif images.

Input

0101

bam clean align

removes unused references from header of sorted BAM/CRAM files.

Input

01

Output

bam versions

bamclipper

primer clipping genomics bam

This module is used to clip primer sequences from your alignments.

Input

0123

Output

bam bai versions

bamcmp

filter xenograft host graft contamination mouse

Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).

Input

012

Output

primary_filtered_bam contamination_bam versions

bamstats_generalstats

bam statistics genomics

write your description here

Input

01

Output

json versions

Tools

rrna sequences removal

barrnap uses a hmmer profile to find rrnas in reads or contig fasta files

Input

012

Output

gff versions

bases2fastq

demultiplex element fastq

Demultiplex Element Biosciences bases files

Input

012

impute-info bcftools imputation metrics tags vcf

Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.

Input

01200

Output

vcf tbi csi versions

Tools

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

bcftools plugin impute-info:

Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available

bcftools_pluginscatter

scatter vcf bcf genomics

Split VCF by chunks or regions, creating multiple VCFs.

Input

01200000

Output

scatter tbi csi versions

Tools

pluginscatter:

Split VCF by chunks or regions, creating multiple VCFs.

bcftools_pluginsetgt

setgt bcftools genotype vcf

Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

Input

0120000

Output

vcf tbi csi versions

Tools

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

bcftools plugin setGT:

Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

bcftools_pluginsplit

split vcf genomics

Split VCF by sample, creating single- or multi-sample VCFs.

Input

0120000

Output

vcf tbi csi versions

Tools

pluginsplit:

Split VCF by sample, creating single- or multi-sample VCFs.

bcftools_plugintag2tag

tag2tag bcftools VCF

Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.

Input

01200

Output

vcf tbi csi versions

Tools

view:

Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.

bcftools_query

query variant calling bcftools VCF

Extracts fields from VCF or BCF files and outputs them in user-defined format.

Input

012000

Output

output versions

Tools

query:

Extracts fields from VCF or BCF files and outputs them in user-defined format.

bcftools_reheader

reheader vcf update header

Reheader a VCF file

Input

012301

Output

vcf index versions

Tools

reheader:

Modify header of VCF/BCF files, change sample names.

bcftools_roh

roh biallelic homozygosity autozygosity

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

Input

012010000

Output

roh versions

Tools

roh:

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

bcftools_sort

sorting VCF variant calling

Sorts VCF files

Input

01

Output

vcf tbi csi versions

Tools

sort:

Sort VCF files by coordinates.

bcftools_split

vcf split genomics

Split a vcf file into files per chromosome

Input

012

Output

split_vcf versions

Tools

bcftools:

Sort VCF files by coordinates.

bcftools_stats

variant calling stats VCF

Generates stats from VCF files

Input

0120101010101

Output

stats versions

Tools

stats:

Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.

bcftools_view

variant calling view bcftools VCF

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

Input

012000

Output

vcf tbi csi versions

Tools

view:

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

bcl2fastq

demultiplex illumina fastq

Demultiplex Illumina BCL files

Input

012

Output

fastq fastq_idx undetermined undetermined_idx reports stats interop versions

bclconvert

demultiplex illumina fastq

Demultiplex Illumina BCL files

Input

012

Output

fastq fastq_idx undetermined undetermined_idx reports logs interop versions

beagle5_beagle

phasing imputation genotype

Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers.

Input

010000

Output

vcf log versions

Tools

bioawk fastq fasta sam file manipulation awk

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.

Input

01

Output

output versions

biobambam_bammarkduplicates2

markduplicates bam cram

Locate and tag duplicate reads in a BAM file

Input

01

Output

bam metrics versions

Tools

biobambam:

biobambam is a set of tools for early stage alignment file processing.

biobambam_bammerge

merge bam sorted

Merge a list of sorted bam files

Input

01

Output

bam bam_index checksum versions

Tools

biobambam:

biobambam is a set of tools for early stage alignment file processing.

biobambam_bamsormadup

markduplicates sort bam cram

Parallel sorting and duplicate marking

Input

0101

Output

bam bam_index cram metrics versions

Tools

biobambam:

biobambam is a set of tools for early stage alignment file processing.

biohansel

Salmonella enterica subtyping prokaryote

Use k-mers to rapidly subtype S. enterica genomes

Input

010

Output

summary kmer_results simple_summary versions

biscuit_align

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam

Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.

Input

010101

Output

bam bai versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_blaster

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

Input

010101

Output

bam bai versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

samblaster:

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout.

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

biscuit_bsconv

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam filter

Summarize and/or filter reads based on bisulfite conversion rate

Input

01010101

Output

bam versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_epiread

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bam

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

Input

0101010101

Output

bed versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_index

biscuit DNA methylation WGBS scWGBS bisulfite sequencing index reference fasta

Indexes a reference genome for use with Biscuit

Input

01

Output

index versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_mergecg

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner bed

Merges methylation information for opposite-strand C's in a CpG context

Input

010101

Output

bed versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_pileup

bisulfite DNA methylation pileup variant calling WGBS scWGBS bam vcf

Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants

Input

012340101

Output

vcf versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_qc

biscuit DNA methylation WGBS scWGBS bisulfite sequencing index BAM quality control

Perform basic quality control on a BAM file generated with Biscuit

Input

010101

Output

reports versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

biscuit_vcf2bed

biscuit DNA methylation WGBS scWGBS bisulfite sequencing aligner vcf

Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.

Input

01

Output

bed versions

Tools

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

bismark_align

bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam

Performs alignment of BS-Seq reads using bismark

Input

010101

Output

bam report unmapped versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_coverage2cytosine

bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph

Relates methylation calls back to genomic cytosine contexts.

Input

010101

Output

coverage report summary versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_deduplicate

bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam

Removes alignments to the same position in the genome from the Bismark mapping output.

Input

01

Output

bam report versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_genomepreparation

bismark 3-letter genome index methylation 5mC methylseq bisulphite bisulfite fasta

Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.

Input

01

Output

index versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_methylationextractor

bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph

Extracts methylation information for individual cytosines from alignments.

Input

0101

Output

bedgraph methylation_calls coverage report mbias versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_report

bismark qc methylation 5mC methylseq bisulphite bisulfite report

Collects bismark alignment reports

Input

01234

Output

report versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

bismark_summary

bismark qc methylation 5mC methylseq bisulphite bisulfite report summary

Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.

Input

00000

Output

summary versions

Tools

bismark:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

blast_blastdbcmd

fasta blast database retrieval identifier

Retrieve entries from a BLAST database

Input

01201

Output

fasta text versions

Tools

blast:

BLAST finds regions of similarity between biological sequences.

blast_blastn

fasta blast blastn DNA sequence

Queries a BLAST DNA database

Input

0101

Output

txt versions

Tools

blast:

BLAST finds regions of similarity between biological sequences.

blast_blastp

fasta blast blastp protein

BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database

Input

01010

Output

xml tsv csv versions

Tools

blast:

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

blast_makeblastdb

fasta blast database

Builds a BLAST database

Input

01

Output

db versions

Tools

blast:

BLAST finds regions of similarity between biological sequences.

blast_tblastn

fasta blast tblastn DNA sequence

Queries a BLAST DNA database

Input

0101

Output

txt versions

Tools

blast:

Protein to Translated Nucleotide BLAST.

blast_updateblastdb

fasta blast download database

Downloads a BLAST database from NCBI

Input

01

Output

db versions

Tools

quality control genome transcriptome proteome

Benchmarking Universal Single Copy Orthologs

Input

metafastamodelineagebusco_lineages_pathconfig_file

Output

meta batch_summary short_summaries_txt short_summaries_json busco_dir full_table missing_busco_list single_copy_proteins seq_dir translated_proteins versions

busco_busco

quality control genome transcriptome proteome

Benchmarking Universal Single Copy Orthologs

Input

0100000

Output

batch_summary short_summaries_txt short_summaries_json log full_table missing_busco_list single_copy_proteins seq_dir translated_dir busco_dir downloaded_lineages versions

Tools

busco:

BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.

busco_generateplot

genome fasta annotation busco transcriptome quality control

BUSCO plot generation tool

Input

0

Output

png versions

Tools

busco:

BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.

busco_phylogenomics

phylogenies orthologs alignment

Construct species phylogenies using BUSCO proteins

Input

01

Output

gene_trees supermatrix versions

Tools

busco:

Construct species phylogenies using BUSCO proteins

bwa_aln

bwa aln short-read align reference fasta map fastq

Find SA coordinates of the input reads for bwa short-read mapping

Input

0101

Output

sai versions

Tools

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwa_index

index fasta genome reference

Create BWA index for reference genome

Input

01

Output

index versions

Tools

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwa_mem

mem bwa alignment map fastq bam sam

Performs fastq alignment to a fasta reference using BWA

Input

0101010

Output

bam cram csi crai versions

Tools

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwa_sampe

bwa aln short-read align reference fasta map sam bam

Convert paired-end bwa SA coordinate files to SAM format

Input

01201

Output

bam versions

Tools

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwa_samse

bwa aln short-read align reference fasta map sam bam

Convert bwa SA coordinate file to SAM format

Input

01201

Output

bam versions

Tools

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwamem2_index

index fasta genome reference

Create BWA-mem2 index for reference genome

Input

01

Output

index versions

Tools

bwamem2:

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwamem2_mem

mem bwa alignment map fastq bam sam

Performs fastq alignment to a fasta reference using BWA

Input

0101010

Output

sam bam cram crai csi versions

Tools

bwa:

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

bwameme_index

index fasta genome reference

Create BWA-MEME index for reference genome

Input

01

Output

index versions

Tools

bwameme:

Faster BWA-MEM2 using learned-index

bwameme_mem

mem bwa bwamem2 bwameme alignment map fastq bam sam cram

Performs fastq alignment to a fasta reference using BWA-MEME

Input

010101000

Output

sam bam cram crai csi versions

Tools

bwameme:

Faster BWA-MEM2 using learned-index

bwameth_align

bwameth alignment 3-letter genome map methylation 5mC methylseq bisulphite bisulfite fastq bam

Performs alignment of BS-Seq reads using bwameth

Input

010101

Output

bam versions

Tools

bwameth:

Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.

bwameth_index

bwameth 3-letter genome index methylseq bisulphite bisulfite fasta

Performs indexing of c2t converted reference genome

Input

01

Output

index versions

Tools

bwameth:

Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.

cadd

cadd annotate variants

CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

Input

010

Output

tsv versions

cafe

gene phylogeny genomics

Analysis of gene family evolution

Input

010

Output

cafe versions cafe_base_count cafe_significant_trees cafe_report cafe_results

calder2

calder2 genome topology compartments domains hi-c

Hierarchical Hi-C compartment computation

Input

010

highly_multiplexed_imaging cell_type_identification cell_phenotyping image_analysis mcmicro machine_learning

Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth

Input

01000

Output

celltypes quality versions

cellbender_merge

single-cell scRNA-seq ambient RNA removal

Module to use CellBender to remove ambient RNA from single-cell RNA-seq data

Input

0123

Output

h5ad versions

Tools

cellbender:

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

cellbender_removebackground

single-cell scRNA-seq ambient RNA removal

Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data

Input

01

Output

h5 filtered_h5 posterior_h5 barcodes metrics report pdf log checkpoint versions

Tools

QC Illumina genomics

A simple program to parse Illumina NGS data and check it for quality criteria

Input

010

Output

report versions

checkv_downloaddatabase

checkv checkm mag metagenome quality isolates virus completeness contamination download database

Construct the database necessary for checkv's quality assessment

Input

NO input

Output

checkv_db versions

Tools

checkv:

Assess the quality of metagenome-assembled viral genomes.

checkv_endtoend

checkv checkm mag metagenome quality isolates virus completeness contamination

Assess the quality of metagenome-assembled viral genomes.

Input

010

Output

quality_summary completeness contamination complete_genomes proviruses viruses versions

Tools

checkv:

Assess the quality of metagenome-assembled viral genomes.

checkv_updatedatabase

checkv checkm mag metagenome quality isolates virus completeness contamination

Construct the database necessary for checkv's quality assessment

Input

010

Output

checkv_db versions

Tools

checkv:

Assess the quality of metagenome-assembled viral genomes.

chewbbaca_createschema

cgMLST WGS genomics

Create a schema to determine the allelic profiles of a genome

Input

0100

Output

schema cds_coordinates invalid_cds versions

Tools

chewbbaca:

A complete suite for gene-by-gene schema creation and strain identification.

chopper

filter trimming fastq nanopore qc

Filter and trim long read data.

Input

010

Output

fastq versions

Tools

zcat:

zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.

gzip:

Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).

chromap_chromap

chromap alignment map fastq bam sam hi-c atac-seq chip-seq trimming duplicate removal

Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.

Input

0101010000

Output

bed bam tagAlign pairs versions

Tools

chromap:

Fast alignment and preprocessing of chromatin profiles

chromap_index

index fasta genome reference

Indexes a fasta reference genome ready for chromatin profiling.

Input

01

Output

index versions

Tools

sort example genomics

binning of metagenomic sequences

Input

01

Output

fasta bins fm index links result versions

clipkit

sort example genomics

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.

Input

010

Output

clipkit log versions

clippy

iCLIP eCLIP CLIP

Runs the Clippy CLIP peak caller

Input

0100

Output

peaks summits intergenic_gtf versions

clonalframeml

fasta multiple sequence alignment recombination

Predict recomination events in bacterial genomes

Input

012

Output

emsim em status newick fasta pos_ref versions

clustalo_align

alignment MSA genomics

Align sequences using Clustal Omega

Input

010100000

Output

alignment versions

Tools

clustalo:

Latest version of Clustal: a multiple sequence alignment program for DNA or proteins

pigz:

Parallel implementation of the gzip algorithm.

clustalo_guidetree

guide tree msa newick

Renders a guidetree in clustalo

Input

01

Output

tree versions

Tools

clustalo:

Latest version of Clustal: a multiple sequence alignment program for DNA or proteins

cmseq_polymut

polymut polymorphic mags assembly polymorphic sites estimation protein coding genes cmseq bam coverage

Calculates polymorphic site rates over protein coding genes

Input

01234

Output

polymut versions

Tools

cmseq:

Set of utilities on sequences and BAM files

cnvkit_access

cvnkit access fasta copy number

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

Input

0101

Output

bed versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_antitarget

cvnkit antitarget cnv copy number

Derive off-target (“antitarget”) bins from target regions.

Input

01

Output

bed versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_batch

cnvkit bam fasta copy number

Copy number variant detection from high-throughput sequencing data

Input

012010101010

Output

bed cnn cnr cns pdf png versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_call

cnvkit bam fasta copy number

Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number

Input

012

Output

cns versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_export

cnvkit copy number export

Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.

Input

01

Output

output versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_genemetrics

cnvkit bam fasta copy number

Copy number variant detection from high-throughput sequencing data

Input

012

Output

tsv cnn versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_reference

cnvkit reference cnv copy number

Compile a coverage reference from the given files (normal samples).

Input

000

Output

cnn versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit_target

cnvkit target cnv copy number

Transform bait intervals into targets more suitable for CNVkit.

Input

0101

Output

bed versions

Tools

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvnator_cnvnator

cnvnator cnv cna

CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.

Input

012010101

Output

root tab versions

Tools

cnvnator:

Tool for calling copy number variations.

cnvnator_convert2vcf

cnvnator cnv cna

convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.

Input

01

Output

vcf versions

Tools

cnvnator:

Tool for calling copy number variations.

cnvpytor_callcnvs

CNV call wgs

Command line tool for calling CNVs in whole genome sequencing data

Input

010

Output

pytor versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_histogram

cnv calling histogram read depth

calculates read depth histograms

Input

010

Output

pytor versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_importreaddepth

read depth cnv cna call

command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.

Input

01200

Output

pytor versions

Tools

cnvpytor -rd:

calling CNVs using read depth

cnvpytor_partition

cnv calling partition histograms read depth

partitioning read depth histograms

Input

010

Output

pytor versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_view

cnv calling vcf

view function to generate vcfs

Input

0100

Output

vcf tsv xls versions

Tools

cnvpytor:

calling CNVs using read depth

cobrameta

cobra contig scaffold assembly extension virus phage

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Input

01010101000

Output

self_circular extended_circular extended_partial extended_failed orphan_end all_cobra_assemblies joining_summary log versions

Tools

cobra-meta:

COBRA is a tool to get higher quality viral genomes assembled from metagenomes.

cobs_classicconstruct

COBS index k-mer index bloom filter

Builds a classic bloom filter COBS index

Input

01

Output

index versions

Tools

cobs:

Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

cobs_compactconstruct

COBS index k-mer index bloom filter

Builds a compact bloom filter COBS index

Input

01

Output

index versions

Tools

cobs:

Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

concoct_concoct

contigs fragment mags binning concoct kmer nucleotide composition metagenomics bins

Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples

Input

012

Output

args_txt clustering_csv log_txt original_data_csv pca_components_csv pca_transformed_csv versions

Tools

concoct:

Clustering cONtigs with COverage and ComposiTion

concoct_concoctcoveragetable

contigs fragment mags binning bed bam subcontigs coverage

Generate the input coverage table for CONCOCT using a BEDFile

Input

0123

Output

tsv versions

Tools

concoct:

Clustering cONtigs with COverage and ComposiTion

concoct_cutupfasta

contigs fragment mags binning fasta cut cut up

Cut up fasta file in non-overlapping or overlapping parts of equal length.

Input

010

Output

fasta bed versions

Tools

concoct:

Clustering cONtigs with COverage and ComposiTion

concoct_extractfastabins

contigs fragment mags binning fasta cut cut up bins merge

Creates a FASTA file for each new cluster assigned by CONCOCT

Input

012

Output

fasta versions

Tools

concoct:

Clustering cONtigs with COverage and ComposiTion

concoct_mergecutupclustering

contigs fragment mags binning fasta cut cut up merge

Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py

Input

01

Output

csv versions

Tools

UNet TMA dearray Segmentation Cores

Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.

Input

01

Output

cores masks tma_map centroids versions

coverm_contig

mapping genomics metagenomics coverage

Map reads to contigs and estimate coverage

Input

010100

Output

coverage versions

Tools

coverm:

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications

crabz_compress

compression gzip zlib

Compress files with crabz

Input

01

Output

archive versions

Tools

crabz:

Like pigz, but rust

crabz_decompress

decompression gzip zlib

Decompress files with crabz

Input

01

Output

file versions

Tools

crabz:

Like pigz, but rust

crisprcleanr_normalize

sort CNV correction CRISPR

remove false positives of functional crispr genomics due to CNVs

Input

01200

Output

norm_count_file versions

Tools

cutesv structural-variant calling sv

structural-variant calling with cutesv

Input

01201

visualisation tsv csv

Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.

Input

0

Output

report versions

decoupler

enrichment omics biological activity functional analysis prior knowledge

decoupler is a package containing different statistical methods to extract biological activities from omics data within a unified framework. It allows to flexibly test any enrichment method with any prior knowledge resource and incorporates methods that take into account the sign and weight. It can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

Input

010

variant calling machine learning neural network

DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.

Input

0123401010101

variant calling machine learning neural network

(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

012301010101

Output

vcf vcf_tbi gvcf gvcf_tbi versions

deepvariant_callvariants

variant calling machine learning neural network

Call variants from the examples produced by make_examples

Input

01

Output

call_variants_tfrecords versions

Tools

deepvariant:

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

deepvariant_makeexamples

variant calling machine learning neural network

Transforms the input alignments to a format suitable for the deep neural network variant caller

Input

012301010101

Output

examples gvcf small_model_calls versions

Tools

deepvariant:

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

deepvariant_postprocessvariants

variant calling machine learning neural network

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

01234010101

Output

vcf vcf_tbi gvcf gvcf_tbi versions

Tools

deepvariant:

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

deepvariant_rundeepvariant

variant calling machine learning neural network

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

012301010101

Output

vcf vcf_tbi gvcf gvcf_tbi versions

Tools

deepvariant:

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

deepvariant_vcfstatsreport

variant calling machine learning neural network

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

01

Output

report versions

Tools

deepvariant:

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

delly_call

genome structural variants bcf

Call structural variants

Input

0123450101

Output

bcf csi versions

Tools

single-cell doublets doublet_detection

Doublet detection in single-cell RNA-seq data

Input

01

Output

h5ad predictions versions

dragmap_align

alignment map fastq bam sam

Performs fastq alignment to a reference using DRAGMAP

Input

0101010

Output

sam bam cram crai csi log versions

Tools

dragmap:

Dragmap is the Dragen mapper/aligner Open Source Software.

dragmap_hashtable

index fasta genome reference

Create DRAGEN hashtable for reference genome

Input

01

Output

hashmap versions

Tools

fasta Streptococcus pyogenes typing

EMM typing of Streptococcus pyogenes assemblies

Input

01

Output

tsv versions

emu_abundance

metagenomics 16S nanopore

A taxonomic profiler for metagenomic 16S data optimized for error prone long reads.

Input

010

Output

report assignment_report samfile unclassified_fa versions

Tools

site frequency spectrum ancestral alleles derived alleles

estimation of the unfolded site frequency spectrum

Input

0123

Output

sfs_out pvalues_out versions

evigene_tr2aacds

genomics transcript assembly clean polish filter redundant duplicate

Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly

Input

01

Output

dropset okayset versions

Tools

trimming quality control fastq faqcs

Perform adapter and quality trimming on sequencing reads with reporting

Input

01

Output

reads stats debug statspdf reads_fail reads_unpaired log versions

fargene

antibiotic resistance genes ARGs identifier metagenomic contigs

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

Input

010

Output

log txt hmm hmm_genes orfs orfs_amino contigs contigs_pept filtered filtered_pept fragments trimmed spades metagenome tmp versions

fast2q

CRISPRi FASTQ genomics

A program that counts sequence occurrences in FASTQ files.

Input

0101

Output

count_matrix stats distribution_plot reads_plot reads_plot_percentage versions

Tools

2FAST2Q:

2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.

fastani

genome fasta ANI

Alignment-free computation of average nucleotide Identity (ANI)

Input

010

Output

ani versions

fastavalidator

fasta validation genome

"Python C-extension for a simple validator for fasta files. The module emits the validated file or an error log upon validation failure."

Input

01

Output

success_log error_log versions

Tools

phylogenetics newick minimum_evolution distance-based

Distance-based phylogeny with FastME

Input

012

Output

nwk stats matrix bootstrap versions

fastp

trimming quality control fastq

Perform adapter/quality trimming on sequencing reads

Input

010000

Output

reads json html log reads_fail reads_merged versions

fastqc

quality control qc adapters fastq

Run FastQC on sequenced reads

Input

01

Output

html zip versions

fastqe

quality control fastq emoji visualization

fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.

Input

01

SRA ENA GEO metadata fetch public databases

A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.

Input

0

Output

json versions

fgbio_callduplexconsensusreads

umi duplex fgbio

Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.

Input

0100

Output

bam versions

Tools

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

fgbio_callmolecularconsensusreads

UMIs consensus sequence bam

Calls consensus sequences from reads with the same unique molecular tag.

Input

0100

Output

bam versions

Tools

fgbio:

Tools for working with genomic and high throughput sequencing data.

fgbio_collectduplexseqmetrics

UMIs QC bam duplex

Collects a suite of metrics to QC duplex sequencing data.

Input

010

Output

family_sizes duplex_family_sizes duplex_yield_metrics umi_counts duplex_qc duplex_umi_counts versions

Tools

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

r-ggplot2:

ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.

fgbio_fastqtobam

unaligned bam cram

Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads

Input

01

Output

bam cram versions

Tools

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

fgbio_filterconsensusreads

fgbio filter consensus umi duplexumi

Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.

Input

0101000

Output

bam versions

Tools

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

fgbio_groupreadsbyumi

UMI groupreads fgbio

Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. (!) Note: the MQ tag is required on reads with mapped mates (!) This can be added using samblaster with the optional argument --addMateTags.

Input

010

Output

bam histogram versions

Tools

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

fgbio_sortbam

sort bam sam

Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.

Input

01

Output

bam versions

Tools

fgbio:

Tools for working with genomic and high throughput sequencing data.

fgbio_zipperbams

fgbio umi unmapped ubam zipperbams

FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM

Input

01010101

Output

sort reads merging merge mate pairs

Perform merging of mate paired-end sequencing reads

Input

01

demultiplex fastq rust

Demultiplex fastq files

Input

012

genomics cluster genome metagenomics

Cluster genome FASTA files by average nucleotide identity

Input

0123

Output

tsv dereplicated_bins versions

gamma_gamma

gamma gene-calling microbial allele

Gene Allele Mutation Microbial Assessment

Input

010

Output

gamma psl gff fasta versions

Tools

gawk awk txt text file parsing

If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. The job is easy with awk, especially the GNU implementation gawk.

Input

0100

Output

output versions

gecco_run

bgc detection metagenomics contigs

GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).

Input

0120

Output

genes features clusters gbk json versions

Tools

gecco:

Biosynthetic Gene Cluster prediction with Conditional Random Fields.

gem2_gem2bedmappability

mappability bedgraph index gem

Convert a mappability file to bedgraph format

Input

0101

Output

bedgraph sizes versions

Tools

gem2:

GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.

gem2_gemindexer

fasta index reference mappability

Create a GEM index from a FASTA file

Input

01

Output

index log versions

Tools

gem2:

GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.

gem2_gemmappability

mappability gem index reference

Define the mappability of a reference

Input

010

Output

map versions

Tools

gem2:

GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.

gem3_gem3indexer

fastq genomics mappability

Create a GEM index from a FASTA file

Input

01

Output

index info versions

Tools

gem3:

The GEM indexer (v3).

gem3_gem3mapper

fastq genomics mappability

Performs fastq alignment to a fasta reference using using gem3-mapper

Input

01010

Output

bam versions

Tools

genome size genome heterozygosity repeat content

Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach

Input

01

Output

linear_plot_png transformed_linear_plot_png log_plot_png transformed_log_plot_png model summary lookup_table fitted_histogram_png versions

genotyphi_parse

genotype Salmonella Typhi Mykrobe

Genotype Salmonella Typhi from Mykrobe results

Input

01

Output

tsv versions

Tools

genotyphi:

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

genrich

peak-calling ChIP-seq ATAC-seq

Peak-calling for ChIP-seq and ATAC-seq enrichment experiments

Input

0120

gfa graph pangenome variation graph

Collapse walk-preserving shared affixes in variation graphs in GFA format

Input

01

transcripts gtf merge compare

Compare, merge, annotate and estimate accuracy of generated gtf files

Input

0101201

merge gvcf joint-variant-calling

merge gVCF files and perform joint variant calling

Input

0101

sort example genomics

Sort GTF files in chr/pos/feature order

Input

0

gunzip compression decompression

Compresses and decompresses files.

Input

01

Output

gunzip versions

gvcftools_extractvariants

gvcftools extract_variants extractvariants gvcf vcf

Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

Input

01

Output

vcf versions

Tools

ibd hbd beagle

The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.

Input

0100

fasta serotype Haemophilus influenzae

Identify cap locus serotype and structure in your Haemophilus influenzae assemblies

Input

0100

Output

gbk svg tsv versions

hicexplorer_hicpca

eigenvectors PCA hicPCA

Computes PCA eigenvectors for a Hi-C matrix.

Input

01

Output

results pca1 pca2 versions

Tools

hicexplorer:

Set of programs to process, analyze and visualize Hi-C and capture Hi-C data

hifiasm

genome assembly haplotype resolution phasing PacBio HiFi long reads

Whole-genome assembly using PacBio HiFi reads

Input

012012012

hmmer hmmsearch rank

R script that scores output from multiple runs of hmmer/hmmsearch

Input

01

Output

hmmrank versions

Tools

hmmer:

Biosequence analysis using profile hidden Markov models

R:

A Language and Environment for Statistical Computing

Tidyverse:

Tidyverse: R packages for data science

hmmer_hmmsearch

Hidden Markov Model HMM hmmer hmmsearch

search profile(s) against a sequence database

Input

012345

Output

output alignments target_summary domain_summary versions

Tools

hmmer:

Biosequence analysis using profile hidden Markov models

hmtnote_annotate

hmtnote mitochondria annotation

Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline

Input

01

Output

vcf versions

Tools

hmtnote:

Human mitochondrial variants annotation using HmtVar.

homer_annotatepeaks

annotations peaks bed

Annotate peaks with HOMER suite

Input

0100

Output

txt stats versions

Tools

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

homer_findpeaks

annotation peaks enrichment

Find peaks with HOMER suite

Input

010

Output

txt versions

Tools

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

homer_maketagdirectory

peaks bed bam sam

Create a tag directory with the HOMER suite

Input

010

Output

tagdir taginfo versions

Tools

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

DESeq2:

Differential gene expression analysis based on the negative binomial distribution

edgeR:

Empirical Analysis of Digital Gene Expression Data in R

homer_makeucscfile

peaks bed bedGraph

Create a UCSC bed graph with the HOMER suite

Input

01

Output

bedGraph versions

Tools

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

homer_pos2bed

peaks bed pos

Converting from HOMER peak to BED file formats

Input

01

Output

bed versions

Tools

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

hostile_fetch

hostile decontamination human removal download

Downloads required reference genomes for Hostile

Input

NO input

Output

reference versions

Tools

umi fastq deduplication hamming-distance clustering

HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.

Input

0101

demultiplex lexogen fastq

Demultiplex paired-end FASTQ files from QuantSeq-Pool

Input

012

Output

fastq undetermined stats versions

idr

IDR peaks ChIP-seq ATAC-seq

Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible Discovery Rate)

Input

000

Output

idr log png versions

igv_js

igv igv.js js genome browser

igv.js is an embeddable interactive genome visualization component

Input

012

Output

browser align_files index_files versions

Tools

Immune Deconvolution RNA-seq Bioinformatics Tools Computational Immunology

Perform immune cell deconvolution using RNA-seq data and various computational methods.

Input

01230

Output

deconv_table deconv_plots versions

instrain_compare

instrain compare align diversity coverage

Strain-level comparisons across multiple inStrain profiles

Input

0120

Output

compare comparisons_table pooled_snv snv_keys snv_info versions

Tools

instrain:

Calculation of strain-level metrics

instrain_profile

instrain metagenomics population genomics profile

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

Input

01000

Output

profile snvs gene_info genome_info linkage mapping_info scaffold_info versions

Tools

phylogeny newick maximum likelihood

Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.

Input

012000000000000

Output

phylogeny report mldist lmap_svg lmap_eps lmap_quartetlh sitefreq_out bootstrap state contree nex splits suptree alninfo partlh siteprob sitelh treels rate mlrate exch_matrix log versions

irescue

scRNA-seq transposons repeats

Quantification of transposable elements expression in scRNA-seq

Input

0100

Output

versions results counts log tmp

islandpath

genomes genomic islands prediction

Genomic island prediction in bacterial and archaeal genomes

Input

01

jasminesv jasmine structural variants vcf bam

Jointly Accurate Sv Merging with Intersample Network Edges

Input

012301010

Output

vcf versions

jupyternotebook

Python Jupyter jupytext papermill notebook reports

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

Input

0100

Output

report artifacts versions

Tools

jupytext:

Jupyter notebooks as plain text scripts or markdown documents

papermill:

Parameterize, execute, and analyze notebooks

nbconvert:

Parameterize, execute, and analyze notebooks

jvarkit_dict2xml

vcf bcf bed dict dictionary fasta fai

Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)

Input

01

Output

bed versions

Tools

jvarkit:

bam cram depth coverage xml svg visualization

Plot whole genome coverage from BAM/CRAM file as SVG

Input

012010101

Output

output versions

Tools

jvarkit:

Java utilities for Bioinformatics.

kaiju_kaiju

classify metagenomics fastq taxonomic profiling

Taxonomic classification of metagenomic sequence data using a protein reference database

Input

010

Output

results versions

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kaiju_kaiju2krona

taxonomy visualisation krona chart metagenomics

Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.

Input

010

Output

txt versions

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kaiju_kaiju2table

classify metagenomics taxonomic profiling

write your description here

Input

0100

Output

summary versions

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kaiju_mergeoutputs

classify metagenomics fastq taxonomic profiling

Merge two tab-separated output files of Kaiju and Kraken in the column format

Input

0120

Output

merged versions

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kaiju_mkfmi

classify metagenomics fastq taxonomic profiling database index

Make Kaiju FMI-index file from a protein FASTA file

Input

010

Output

fmi bwt sa versions

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kalign_align

alignment MSA genomics

Aligns sequences using kalign

Input

010

Output

alignment versions

Tools

kalign:

Kalign is a fast and accurate multiple sequence alignment algorithm.

kallisto_index

kallisto kallisto/index index

Create kallisto index

Input

01

Output

index versions

Tools

kallisto:

Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

kallisto_quant

quant kallisto pseudoalignment

Computes equivalence classes for reads and quantifies abundances

Input

01010000

Output

results json_info log versions

Tools

kallisto:

Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

kallistobustools_count

scRNA-seq count single-cell kallisto bustools

quantifies scRNA-seq data from fastq files using kb-python.

Input

01000000

Output

count versions matrix

Tools

kb:

kallisto and bustools are wrapped in an easy-to-use program called kb

kallistobustools_ref

scRNA-seq count single-cell kallisto bustools index

index creation for kb count quantification of single-cell data.

Input

000

Output

versions index t2g cdna intron cdna_t2c intron_t2c

Tools

kb:

kallisto|bustools (kb) is a tool developed for fast and efficient processing of single-cell OMICS data.

kat_hist

k-mer histogram count

Creates a histogram of the number of distinct k-mers having a given frequency.

Input

01

Output

hist json png ps pdf jellyfish_hash versions

Tools

kat:

KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts

khmer_normalizebymedian

digital normalization khmer k-mer counting

Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.

Input

000

Output

reads versions

Tools

khmer:

khmer k-mer counting library

khmer_uniquekmers

khmer k-mer effective genome size

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Input

00

Output

report kmers versions

Tools

fasta kegg kofamscan

Produces annotation using kofamscan against a Profile database and a KO list

Input

0100

Output

txt tsv versions

kraken2_add

metagenomics db classification build kraken2 add

Adds fasta files to a Kraken2 taxonomic database

Input

010000

Output

db versions

Tools

kraken2:

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

kraken2_build

metagenomics db classification build kraken2

Builds Kraken2 database

Input

010

Output

db versions

Tools

kraken2:

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

kraken2_buildstandard

metagenomics db classification build kraken2 standard download

Downloads and builds Kraken2 standard database

Input

0

Output

db versions

Tools

kraken2:

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

kraken2_kraken2

classify metagenomics fastq db

Classifies metagenomic sequence data

Input

01000

Output

classified_reads_fastq unclassified_reads_fastq classified_reads_assignment report versions

Tools

kraken2:

Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads

krakentools_combinekreports

kraken krakentools metagenomics table combining merging

Takes multiple kraken-style reports and combines them into a single report file

Input

01

Output

txt versions

Tools

krakentools:

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.

krakentools_extractkrakenreads

kraken2 krakentools metagenomics

Extract reads classified at any user-specified taxonomy IDs.

Input

0010101

Output

extracted_kraken2_reads versions

Tools

krakentools:

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.

krakentools_kreport2krona

kraken krona metagenomics visualization

Takes a Kraken report file and prints out a krona-compatible TEXT file

Input

01

Output

txt versions

Tools

krakentools:

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.

krakenuniq_build

metagenomics krakenuniq database build ncbi

Download and build (custom) KrakenUniq databases

Input

01230

Output

db versions

Tools

krakenuniq:

Metagenomics classifier with unique k-mer counting for more specific results

krakenuniq_download

metagenomics krakenuniq database download ncbi

Download KrakenUniq databases and related fles

Input

0

Output

output versions

Tools

krakenuniq:

Metagenomics classifier with unique k-mer counting for more specific results

krakenuniq_preloadedkrakenuniq

classify metagenomics kmers fastq db

Classifies metagenomic sequence data using unique k-mer counts

Input

012000000

Output

classified_reads unclassified_reads classified_assignment report versions

Tools

krakenuniq:

Metagenomics classifier with unique k-mer counting for more specific results

krona_kronadb

database taxonomy krona

KronaTools Update Taxonomy downloads a taxonomy database

Input

NO input

Output

db versions

Tools

krona:

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

krona_ktimporttaxonomy

plot taxonomy interactive html visualisation krona chart

KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.

Input

010

Output

html versions

Tools

krona:

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

krona_ktimporttext

plot taxonomy interactive html visualisation krona chart metagenomics

Creates a Krona chart from text files listing quantities and lineages.

Input

01

Output

html versions

Tools

krona:

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

krona_ktupdatetaxonomy

database taxonomy krona visualisation

KronaTools Update Taxonomy downloads a taxonomy database

Input

NO input

Output

db versions

Tools

krona:

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

last_dotplot

LAST plot pair alignment MAF

Makes a dotplot (Oxford Grid) of pair-wise sequence alignments

Input

0120100

Output

gif png versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_lastal

LAST align fastq fasta

Aligns query sequences to target sequences indexed with lastdb

Input

0120

Output

maf multiqc versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_lastdb

LAST index fasta fastq

Prepare sequences for subsequent alignment with lastal.

Input

01

Output

index versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_mafconvert

LAST convert alignment MAF

Converts MAF alignments in another format.

Input

012010101

Output

axt_gz bam blast_gz blasttab_gz chain_gz cram gff_gz html_gz psl_gz sam_gz tab_gz versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_mafswap

LAST reorder alignment MAF

Reorder alignments in a MAF file

Input

01

Output

maf versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_postmask

LAST mask alignment MAF

Post-alignment masking

Input

01

Output

maf versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_split

LAST split spliced alignment MAF

Find split or spliced alignments in a MAF file

Input

01

Output

maf multiqc versions

Tools

last:

LAST finds & aligns related regions of sequences.

last_train

LAST train fastq fasta

Find suitable score parameters for sequence alignment

Input

010

Output

param_file multiqc versions

Tools

last:

LAST finds & aligns related regions of sequences.

learnmsa_align

alignment MSA genomics

Align sequences using learnMSA

Input

01

Output

alignment versions

Tools

learnmsa:

learnMSA: Learning and Aligning large Protein Families

leehom

ancient DNA adapter removal clipping trimming merging collapsing preprocessing bayesian

Bayesian reconstruction of ancient DNA fragments

Input

01

genome annotation gff3 gtf liftover

Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same, or closely-related species

Input

01000

Output

gff3 polished_gff3 unmapped_txt versions

lima

isoseq ccs primer pacbio barcode

lima - The PacBio Barcode Demultiplexer and Primer Remover

Input

010

Output

counts report summary versions bam pbi fasta fastagz fastq fastqgz xml json clips guess

limma_differential

differential expression microarray limma

runs a differential expression analysis with Limma

Input

0123012

Output

results md_plot rdata model session_info normalised_counts versions

Tools

genomics annotation parallel repeat long terminal retrotransposon retrotransposon

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

Input

01

Output

scn gff versions

Tools

LTR_FINDER_parallel:

A Perl wrapper for LTR_FINDER

LTR_Finder:

An efficient program for finding full-length LTR retrotranspsons in genome sequences

ltrharvest

genomics genome annotation repeat transposons retrotransposons

Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest utility included in the EDTA toolchain

Input

01

Output

gff3 scn versions

Tools

LTR_HARVEST_parallel:

A Perl wrapper for LTR_harvest

gt:

The GenomeTools genome analysis system

ltrretriever

genomics annotation repeat long terminal repeat retrotransposon

Identifies LTR retrotransposons using LTR_retriever

Input

metagenomeharvestfindermgescannon_tgca

Output

meta log pass_list pass_list_gff ltrlib annotation_out annotation_gff versions

Tools

LTR_retriever:

Sensitive and accurate identification of LTR retrotransposons

ltrretriever_lai

genomics annotation repeat long terminal retrotransposon retrotransposon stats qc

Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments

Input

01000

Output

log lai_out versions

Tools

lai:

Assessing genome assembly quality using the LTR Assembly Index (LAI)

ltrretriever_ltrretriever

genomics annotation repeat long terminal repeat retrotransposon

Identifies LTR retrotransposons using LTR_retriever

Input

010000

Output

log pass_list pass_list_gff ltrlib annotation_out annotation_gff versions

Tools

LTR_retriever:

Sensitive and accurate identification of LTR retrotransposons

macrel_contigs

AMP antimicrobial peptides genome mining metagenomes peptide prediction

A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.

Input

01

Output

smorfs all_orfs amp_prediction readme_file log_file versions

Tools

macrel:

A pipeline for AMP (antimicrobial peptide) prediction

macs2_callpeak

alignment atac-seq chip-seq peak-calling

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

Input

0120

Output

peak xls versions gapped bed bdg

Tools

macs2:

Model Based Analysis for ChIP-Seq data

macs3_callpeak

alignment atac-seq chip-seq peak-calling

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

Input

0120

Output

peak xls versions gapped bed bdg

Tools

macs3:

Model Based Analysis for ChIP-Seq data

mafft

fasta msa multiple sequence alignment

Multiple sequence alignment using MAFFT

Input

0101010101010

Output

fas versions

Tools

pigz:

Parallel implementation of the gzip algorithm.

mafft_align

fasta msa multiple sequence alignment

Multiple sequence alignment using MAFFT

Input

0101010101010

Output

fas versions

Tools

mafft:

Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

pigz:

Parallel implementation of the gzip algorithm.

mafft_guidetree

fasta msa guide tree

Guide tree rendering using MAFFT

Input

01

Output

tree versions

Tools

mafft:

Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

mageck_count

sort functional genomics sgRNA CRISPR-Cas9

mageck count for functional genomics, reads are usually mapped to a specific sgRNA

Input

010

Output

count norm versions

Tools

mageck:

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.

mageck_mle

sort maximum-likelihood CRISPR

maximum-likelihood analysis of gene essentialities computation

Input

010

Output

gene_summary sgrna_summary versions

Tools

mageck:

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.

mageck_test

sort rra CRISPR

Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.

Input

01

Output

gene_summary sgrna_summary r_script versions

Tools

mageck:

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.

magus_align

MSA alignment genomics graph

Multiple Sequence Alignment using Graph Clustering

Input

01010

Output

alignment versions

Tools

magus:

Multiple Sequence Alignment using Graph Clustering

magus_guidetree

MSA guidetree genomics graph

Multiple Sequence Alignment using Graph Clustering

Input

01

Output

tree versions

Tools

magus:

Multiple Sequence Alignment using Graph Clustering

malt_build

malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome database

MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.

Input

0000

Output

index versions log

Tools

malt:

A tool for mapping metagenomic data

malt_run

malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome

MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.

Input

010

Output

rma6 alignments log versions

Tools

ancient DNA DNA damage NGS damage patterns bam

Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Input

010

Output

runtime_log fragmisincorporation_plot length_plot misincorporation lgdistribution dnacomp stats_out_mcmc_hist stats_out_mcmc_iter stats_out_mcmc_trace stats_out_mcmc_iter_summ_stat stats_out_mcmc_post_pred stats_out_mcmc_correct_prob dnacomp_genome rescaled pctot_freq pgtoa_freq fasta folder versions

mash_dist

distance estimate reference query

Calculate Mash distances between reference and query sequences

Input

010

Output

dist versions

Tools

mash:

Fast sequence distance estimator that uses MinHash

mash_screen

screen containment contamination taxonomic assignment

Screens query sequences against large sequence databases

Input

0101

Output

screen versions

Tools

mash:

Fast sequence distance estimator that uses MinHash

mash_sketch

mash mash/sketch minhash reduced representations sequences sketch

Creates vastly reduced representations of sequences using MinHash

Input

01

Output

mash stats versions

Tools

mash:

Fast sequence distance estimator that uses MinHash

mashmap

mapper aligner minhash kmer

Mashmap is an approximate long read or contig mapper based on Jaccard similarity

Input

0101

Output

paf versions

mashtree

tree mash fasta fastq

Quickly create a tree using Mash distances

Input

01

Output

tree matrix versions

maxbin2

metagenomics assembly binning maxbin2 de novo assembly mags metagenome-assembled genomes contigs

MaxBin is a software that is capable of clustering metagenomic contigs

Input

0123

Output

binned_fastas summary abundance log marker_counts unbinned_fasta tooshort_fasta marker_bins marker_genes versions

maxquant_lfq

sort proteomics mass-spectroscopy

Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"

Input

0120

Output

maxquant_txt versions

Tools

maxquant:

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.

mcquant

quantification image_analysis mcmicro highly_multiplexed_imaging

Mcquant extracts single-cell data given a multi-channel image and a segmentation mask.

Input

010101

checksum MD5 128 bit

Create MD5 (128-bit) checksums

Input

010

fasta Neisseria meningitidis serotype

Serotyping of Neisseria meningitidis assemblies

Input

01

Output

tsv versions

merfin_hist

assembly evaluation quality completeness

Compare k-mer frequency in reads and assembly to devise the metrics K and QV

Input

0101000

Output

hist log_stderr versions

Tools

assembler short-read de Bruijn

Minia is a short-read assembler based on a de Bruijn graph

Input

01

microrna mirna target prediction

miRanda is an algorithm for finding genomic targets for microRNAs

Input

010

Output

txt versions

mirdeep2_mapper

mirdeep2 mapper RNA sequencing

miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.

Input

0101

Output

outputs versions

Tools

mirdeep2:

miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.

mirdeep2_mirdeep2

mirdeep2 miRNA RNA sequencing

miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.

Input

012010123

Output

outputs versions

Tools

mirdeep2:

miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs. It includes three main scripts: miRDeep2.pl, mapper.pl, and quantifier.pl for comprehensive miRNA detection and quantification.

mirtop_counts

mirna isomir gff

mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples.

Input

0101012

Output

tsv versions

Tools

mirtop:

Small RNA-seq annotation

mirtop_export

mirna isomir gff

mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package

Input

0101012

Output

tsv fasta vcf versions

Tools

mirtop:

Small RNA-seq annotation

mirtop_gff

mirna isomir gff

mirtop gff generates the GFF3 adapter format to capture miRNA variations

Input

0101012

Output

gff versions

Tools

mirtop:

Small RNA-seq annotation

mirtop_stats

mirna isomir gff

mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category.

Input

01

Output

txt log versions

Tools

mirtop:

Small RNA-seq annotation

mirtrace_qc

microRNA smrnaseq QC

A tool for quality control and tracing taxonomic origins of microRNA sequencing data

Input

0120

Output

html json tsv all_fa rnatype_unknown_fa versions

Tools

mirtrace:

miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.

mitohifi_findmitoreference

mitochondrial genome reference genome NCBI

Download a mitochondrial genome to be used as reference for MitoHiFi

Input

01

Output

fasta gb versions

Tools

findMitoReference.py:

Fetch mitochondrial genome in Fasta and Genbank format from NCBI

MITOHIFI_MITOHIFI

mitochondrion chloroplast PacBio

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Input

010000

Output

fasta stats gb gff all_potential_contigs contigs_annotations contigs_circularization contigs_filtering coverage_mapping coverage_plot final_mitogenome_annotation final_mitogenome_choice final_mitogenome_coverage potential_contigs reads_mapping_and_assembly shared_genes versions

Tools

mosdepth bam cram coverage

Calculates genome-wide sequencing coverage.

Input

012301

Output

global_txt summary_txt regions_txt per_base_d4 per_base_bed per_base_csi regions_bed regions_csi quantized_bed quantized_csi thresholds_bed thresholds_csi versions

motus_downloaddb

classify metagenomics fastq taxonomic profiling database download

Download the mOTUs database

Input

0

Output

db versions

Tools

motus:

The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.

motus_merge

classify metagenomics fastq taxonomic profiling merging merge otu table

Taxonomic meta-omics profiling using universal marker genes

Input

0100

Output

txt biom versions

Tools

motus:

Marker gene-based OTU (mOTU) profiling

motus_preplong

classify metagenomics fastq taxonomic profiling

Taxonomic meta-omics profiling using universal marker genes

Input

010

Output

out versions

Tools

motus:

Marker gene-based operational taxonomic unit (mOTU) profiling

motus_profile

classify metagenomics fastq taxonomic profiling

Taxonomic meta-omics profiling using universal marker genes

Input

010

Output

out bam mgc log versions

Tools

motus:

Marker gene-based OTU (mOTU) profiling

msisensor_msi

homoploymer microsatellite MSI instability

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

Input

0123456

Output

output output_dis output_germline output_somatic versions

Tools

msisensor:

MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.

msisensor_scan

homoploymer microsatellite MSI

Scan a reference genome to get microsatellite & homopolymer information

Input

01

Output

txt versions

Tools

msisensor:

MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.

msisensor2_msi

msi microsatellite microsatellite instability tumor cfDNA

msisensor2 detection of MSI regions.

Input

01234500

Output

msi distribution somatic versions

Tools

msisensor2:

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

msisensor2_scan

microsatellite instability detection tumor

msisensor2 detection of MSI regions.

Input

00

Output

scan versions

Tools

msisensor2:

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

msisensorpro_msisomatic

micro-satellite-scan msisensor-pro msi somatic

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

Input

01234500

Output

output_report output_dis output_germline output_somatic versions

Tools

msisensorpro:

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

msisensorpro_scan

micro-satellite-scan msisensor-pro scan

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

Input

01

Output

list versions

Tools

msisensorpro:

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

mtmalign_align

alignment MSA genomics structure

Aligns protein structures using mTM-align

Input

010

Output

alignment structure versions

Tools

mTM-align:

Algorithm for structural multiple sequence alignments

vcf ancient DNA aDNA SNP GATK UnifiedGenotyper SNP table

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

Input

010101010000001

Output

full_alignment info_txt snp_alignment snp_genome_alignment snpstatistics snptable snptable_snpeff snptable_uncertainty structure_genotypes structure_genotypes_nomissing json versions

mummer

align genome fasta

MUMmer is a system for rapidly aligning entire genomes

Input

012

Output

coords versions

muscle

msa multiple sequence alignment phylogeny

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two

Input

01

Output

aligned_fasta phyi phys clustalw html msf tree log versions

muscle5_super5

align msa multiple sequence alignment

Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.

Input

010

Output

alignment versions

Tools

muscle -super5:

Muscle v5 is a major re-write of MUSCLE based on new algorithms.

pigz:

Parallel implementation of the gzip algorithm.

muse_call

variant calling somatic wgs wxs vcf

pre-filtering and calculating position-specific summary statistics using the Markov substitution model

Input

0123401

Output

txt versions

Tools

MuSE:

Somatic point mutation caller based on Markov substitution model for molecular evolution

muse_sump

variant calling somatic wgs wxs vcf

Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants

Input

01012

Output

vcf versions

Tools

bam fasta fastq qc nanopore

Compare multiple runs of long read sequencing data and alignments

Input

01

Output

report_html lengths_violin_html log_length_violin_html n50_html number_of_reads_html overlay_histogram_html overlay_histogram_normalized_html overlay_log_histogram_html overlay_log_histogram_normalized_html total_throughput_html quals_violin_html overlay_histogram_identity_html overlay_histogram_phredscore_html percent_identity_violin_html active_pores_over_time_html cumulative_yield_plot_gigabases_html sequencing_speed_over_time_html stats_txt versions

nanofilt

nanopore filtering QC

Filtering and trimming of Oxford Nanopore Sequencing data

Input

010

Output

filtreads log_file versions

nanolyse

contaminant removal dna

DNA contaminant removal using NanoLyse

Input

010

Output

fastq log versions

nanomonsv_parse

structural variants nanopore cancer genome somatic structural variations mobile element insertions long reads

Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"

Input

012

Output

insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions

Tools

nanomonsv:

nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.

nanoplot

quality control qc fastq sequencing summary nanopore

Run NanoPlot on nanopore-sequenced reads

Input

01

fasta Neisseria gonorrhoeae serotype

Serotyping Neisseria gonorrhoeae assemblies

Input

01

metagenomics statistics coverage complexity

write your description here

Input

metareadsformatmode

Output

meta versions npa npc npl npo

nonpareil_curve

metagenomics statistics coverage complexity redundancy diversity visualisation

Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file

Input

01

Output

png versions

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nonpareil_nonpareil

metagenomics statistics coverage redundancy diversity complexity

Calculate metagenome redundancy curve from FASTQ files

Input

0100

Output

npa npc npl npo versions

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nonpareil_nonpareilcurvesr

metagenomics statistics coverage redundancy diversity complexity multiqc

Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files

Input

01

Output

json tsv csv pdf versions

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nonpareil_set

metagenomics statistics coverage complexity redundancy diversity visualisation

Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image

Input

01

Output

png versions

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nucmer

align nucleotide sequence

NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.

Input

012

cnv bam tumor/normal

Calls CNVs in bam files from tumor patients

Input

0123400

Output

png profile summary versions

openms_decoydatabase

decoy database openms proteomics fasta

Create a decoy peptide database from a standard FASTA database.

Input

01

Output

decoy_fasta versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_filefilter

filter mzML openms proteomics

Filters peptide/protein identification results by different criteria.

Input

01

Output

mzml featurexml consensusxml versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_idfilter

filter idXML openms proteomics

Filters peptide/protein identification results by different criteria.

Input

012

Output

filtered versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_idmassaccuracy

mass_error openms proteomics

Calculates a distribution of the mass error from given mass spectra and IDs.

Input

012

Output

frag_err prec_err versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_idmerger

merge idXML openms proteomics

Merges several idXML files into one idXML file.

Input

01

Output

idxml versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_idripper

split idXML openms proteomics

Split a merged identification file into their originating identification files

Input

01

Output

idxmls versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_idscoreswitcher

switch score idXML openms proteomics

Switches between different scores of peptide or protein hits in identification data

Input

01

Output

idxml versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_peakpickerhires

peak picking mzml openms proteomics

A tool for peak detection in high-resolution profile data (Orbitrap or FTICR)

Input

01

Output

mzml versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms_peptideindexer

refresh idXML openms proteomics

Refreshes the protein references for all peptide hits.

Input

012

Output

indexed_idxml versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openmsthirdparty_cometadapter

search engine fasta mzml openms proteomics

Annotates MS/MS spectra using Comet.

Input

012

Output

idxml pin versions

Tools

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

optitype

hla-typing ILP HLA-I

Perform HLA-I typing of sequencing data

Input

012

Output

hla_type coverage_plot versions

orthofinder

genomics orthogroup orthologs gene duplication tree phylogeny

OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.

Input

0101

Output

orthofinder working versions

paftools_sam2paf

paf bam conversion

A program to convert bam into paf.

Input

01

Output

paf versions

Tools

covid pangolin lineage

Phylogenetic Assignment of Named Global Outbreak LINeages

Input

01

Output

report versions

pangolin_run

covid pangolin lineage run

Phylogenetic Assignment of Named Global Outbreak LINeages

Input

010

Output

report versions

Tools

pangolin:

Phylogenetic Assignment of Named Global Outbreak LINeages

pangolin_updatedata

covid pangolin database lineage updatedata

Phylogenetic Assignment of Named Global Outbreak LINeages

Input

0

Output

db versions

Tools

pangolin:

Phylogenetic Assignment of Named Global Outbreak LINeages

parabricks_applybqsr

bqsr bam GPU-accelerated base quality score recalibration

NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).

Input

0101010101

Output

bam bai versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_dbsnp

annotation dbsnp vcf germline

NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database

Input

0123

Output

vcf versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_deepvariant

variant deep variant vcf haplotypecaller germline

NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.

Input

012301

Output

vcf gvcf versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_fq2bam

align sort bqsr duplicates

NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.

Input

01010101010

Output

bam bai cram crai bqsr_table qc_metrics duplicate_metrics versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_fq2bammeth

align sort bqsr duplicates bwameth

VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence

Input

0101010

Output

bam bai qc_metrics bqsr_table duplicate_metrics versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_genotypegvcf

joint-genotyping gvcf vcf genotypegvcf germline

NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs

Input

0101

Output

vcf versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_haplotypecaller

variant vcf haplotypecaller germline

NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.

Input

012301

Output

vcf gvcf versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_indexgvcf

vcf gvcf tbi idx index GPU-accelerated

NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool.

Input

01

Output

gvcf_index versions

Tools

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

parabricks_mutectcaller

variant vcf mutect2 mutect somatic

NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2.

Input

0123450100

Output

vcf stats versions

Tools

paraphase long-read HiFi

HiFi-based caller for highly homologous genes

Input

0120101

Output

json bam bai vcf vcf_index versions

pasty

bacteria serogroup fasta assembly

Serogroup Pseudomonas aeruginosa assemblies

Input

01

Output

tsv blast details versions

pbbam_pbmerge

pbbam pbmerge bam

The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.

Input

01

Output

bam pbi versions

Tools

pbbam:

PacBio BAM C++ library

pbccs

ccs pacbio isoseq subreads

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

Input

01200

Output

bam pbi report_txt report_json metrics versions

pbmm2_align

align pacbio genomics

Alignment with PacBio's minimap2 frontend

Input

0101

Output

bam versions

Tools

pair-end read merge

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger.

Input

01

Output

assembled unassembled discarded versions

peddy

pedigrees ped family

Manipulation, validation and exploration of pedigrees

Input

0120

Output

html csv ped png versions

peka

motif CLIP iCLIP genomics k-mer

Runs PEKA CLIP peak k-mer analysis

Input

0101000

Output

cluster distribution rtxn pdf tsites oxn clust versions

perbase

bam cram depth

Per-base metrics on BAM/CRAM files.

Input

012012

polishing assembly variant calling

Automatically improve draft assemblies and find variation among strains, including large event detection

Input

010120

Output

improved_assembly vcf change_record tracks_bed tracks_wig versions

pindel_pindel

deletions insertions tandem duplications

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

Input

012000

Output

bp cem del dd int_final inv li rp si td versions

Tools

pindel:

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data

pints_caller

peak-calling CoPRO GRO-cap PRO-cap CAGE NETCAGE RAMPAGE csRNA-seq STRIPE-seq PRO-seq GRO-seq

Main caller script for peak calling

Input

0120

Output

divergent_TREs bidirectional_TREs unidirectional_TREs peakcalling_log versions

Tools

pints:

Peak Identifier for Nascent Transcripts Starts (PINTS)

pirate

gff pan-genome alignment

Pangenome toolbox for bacterial genomes

Input

01

Output

results aln versions

plasmidfinder

fasta fastq plasmid

Identify plasmids in bacterial sequences and assemblies

Input

01

Output

json txt tsv genome_seq plasmid_seq versions

plasmidid

assembly plasmid bacterial

assembles bacterial plasmids

Input

010

fastq serotype Streptococcus pneumoniae

Determine Streptococcus pneumoniae serotype from Illumina paired-end reads

Input

01

fasta genome qc nucleotides

Calculate pairwise nucleotide identity with respect to a reference sequence

Input

01010

Output

valid_fasta invalid_fasta report log versions

presto_filterseq

immcantation airrseq genomics immunoinformatics

Filter reads by quality score.

Input

coexpression correlation proportionality logratio propr corpcor

Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. One can also compute standard correlation coefficients, if required.

Input

01

Output

propr matrix fdr adj warnings session_info versions

Tools

propr:

Logratio methods for omics data

corpcor:

Efficient Estimation of Covariance and (Partial) Correlation

proteinortho

orthology co-orthology homology sequence similarity spectral clustering comparative genomics genomics

Proteinortho is a tool to detect orthologous genes within different species.

Input

01

Output

orthologgroups orthologgraph blastgraph versions

proteus_readproteingroups

proteomics proteus readproteingroups

reads a maxQuant proteinGroups file with Proteus

Input

012

Output

dendro_plot mean_var_plot raw_dist_plot norm_dist_plot raw_rdata norm_rdata raw_tab norm_tab session_info versions

Tools

qc quality control sequencing nanopore

write your description here

Input

01

Output

html json versions

pydamage_analyze

ancient DNA aDNA de novo assembly filtering damage deamination miscoding lesions C to T palaeogenomics archaeogenomics palaeogenetics archaeogenetics

Damage parameter estimation for ancient DNA

Input

012

Output

csv versions

Tools

pydamage:

Damage parameter estimation for ancient DNA

pydamage_filter

ancient DNA aDNA de novo assembly filtering damage deamination miscoding lesions C to T palaeogenomics archaeogenomics palaeogenetics archaeogenetics

Damage parameter estimation for ancient DNA

Input

01

Output

csv versions

Tools

pydamage:

Damage parameter estimation for ancient DNA

pypgx_computecontrolstatistics

pypgx pharmacogenetics controlstatistics

Compute summary statistics for control gene from BAM files.

Input

01200

Output

control_stats versions

Tools

pypgx:

A Python package for pharmacogenomics research

pypgx_createinputvcf

pypgx Pharmacogenetics variants

Call SNVs/indels from BAM files for all target genes.

Input

0120100

Output

vcf tbi versions

Tools

pypgx:

A Python package for pharmacogenomics research

pypgx_preparedepthofcoverage

Pharmacogenetics pypgx SV

Prepare a depth of coverage file for all target genes with SV from BAM files.

Input

01200

Output

coverage versions

Tools

pypgx:

A Python package for pharmacogenomics research

pypgx_runngspipeline

pypgx pharmacogenetics genotyping

PyPGx pharmacogenomics genotyping pipeline for NGS data.

Input

012345010

Output

results cnv_calls consolidated_variants versions

Tools

pypgx:

A Python package for pharmacogenomics research

pyrodigal

sort annotation prediction prokaryote

Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.

Input

010

quast assembly quality contig scaffold

Quality Assessment Tool for Genome Assemblies

Input

010101

Output

results tsv transcriptome misassemblies unaligned versions

quilt_quilt

imputation low-coverage genotype genomics vcf

QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.

Input

sort example genomics

Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data

Input

010101

Output

best_offset offset offset_plot psites codon_coverage_rpf codon_coverage_psite cds_coverage cds_window_coverage ribowaltz_qc versions

ripgrep

search regex patterns

ripgrep recursively searches directories for a regex pattern

Input

0100

Output

txt versions

Tools

pigz:

Parallel implementation of the gzip algorithm.

rmarkdownnotebook

R notebook reports

Render an rmarkdown notebook. Supports parametrization.

Input

0100

Output

report parameterised_notebook artifacts session_info versions

Tools

rmarkdown:

Dynamic Documents for R

roary

gff pan-genome alignment

Calculate pan-genome from annotated bacterial assemblies in GFF3 format

Input

01

assembly hi-c scaffolding long reads salsa salsa2

SALSA, A tool to scaffold long read assemblies with HiC

Input

0120000

Output

fasta agp agp_original_coordinates versions

sam2lca_analyze

LCA alignment bam metagenomics Ancestor multimapper

Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files

Input

0120

Output

csv json bam versions

Tools

sam2lca:

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

sambamba_flagstat

stats flagstat sambamba

Outputs some statistics drawn from read flags.

Input

01

Output

stats versions

Tools

sambamba:

Tools for working with SAM/BAM data

sambamba_markdup

markduplicates duplicates bam

find and mark duplicate reads in BAM file

Input

01

Output

bam bai versions

Tools

sambamba:

process your BAM data faster!

samblaster

sort duplicate marking bam

This module combines samtools and samblaster in order to use samblaster capability to filter or tag SAM files, with the advantage of maintaining both input and output in BAM format. Samblaster input must contain a sequence header: for this reason it has been piped with the "samtools view -h" command. Additional desired arguments for samtools can be passed using: options.args2 for the input bam file options.args3 for the output bam file

Input

01

cat collate fixmate sort markduplicates bam sam cram multi-tool

Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file

Input

0101

Output

bam cram csi crai metrics versions

Tools

samtools_cat:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_collate:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_fixmate:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_sort:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_markdup:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_sort

sort bam sam cram

Sort SAM/BAM/CRAM file

Input

0101

Output

bam cram crai csi versions

Tools

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_stats

statistics counts bam sam cram

Produces comprehensive statistics from SAM/BAM/CRAM file

Input

01201

Output

stats versions

Tools

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

samtools_view

view bam sam cram

filter/convert SAM/BAM/CRAM file

Input

0120100

Output

bam cram sam bai csi crai unselected unselected_index versions

Tools

gwas pangenome prokaryote

Use pangenome outputs for GWAS

Input

0120

Output

csv versions

scramble_clusteranalysis

soft-clipped clusters scramble cluster analysis clusteridentifier

The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier

Input

0100

Output

meis_tab dels_tab vcf versions

Tools

scramble:

Soft Clipped Read Alignment Mapper

scramble_clusteridentifier

bam cram soft-clipped clusters

The cluster_identifier tool of Scramble identifies soft clipped clusters

Input

0120

Output

clusters versions

Tools

scramble:

Soft Clipped Read Alignment Mapper

scvitools_scar

single-cell scRNA-seq ambient RNA removal

Module to use scAR to remove ambient RNA from single-cell RNA-seq data

Input

012

Output

h5ad versions

Tools

scvitools:

scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data

scar:

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics.

scvitools_solo

scvi solo doublets

Detect doublets in single-cell RNA-Seq data

Input

01

Output

h5ad predictions versions

Tools

scvitools:

A scalable toolkit for probabilistic modeling applied to single-cell omics data

seacr_callpeak

peak-caller peaks bedgraph cut&tag cut&run chromatin seacr

Call peaks using SEACR on sequenced reads in bedgraph format

Input

0120

Output

bed versions

Tools

seacr:

SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).

segemehl_align

alignment circrna splicing fusions

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Input

0100

Output

alignment trans_alignments multi_bed single_bed versions

Tools

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

segemehl_index

index circrna splicing fusions

Generate genome indices for segemehl align

Input

0

Output

index versions

Tools

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

semibin_singleeasybin

binning assembly-binning metagenomics

metagenomic binning with self-supervised learning

Input

012

Output

csv model output_fasta recluster_fasta tsv versions

Tools

semibin:

Metagenomic binning with semi-supervised siamese neural network

sentieon_applyvarcal

sentieon applyvarcal varcal VQSR

Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm

Input

0123450101

Output

vcf tbi versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_bwaindex

index fasta genome reference sentieon

Create BWA index for reference genome

Input

01

Output

index versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_bwamem

mem bwa alignment map fastq bam sentieon

Performs fastq alignment to a fasta reference using Sentieon's BWA MEM

Input

01010101

Output

bam_and_bai versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_collectvcmetrics

vcf sentieon genomics

Accelerated implementation of the Picard CollectVariantCallingMetrics tool.

Input

012012010101

Output

metrics summary versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_coveragemetrics

coverage sentieon genomics

Accelerated implementation of the GATK DepthOfCoverage tool.

Input

01201010101

Output

per_locus sample_summary statistics coverage_counts coverage_proportions interval_summary versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_datametrics

metrics bam sentieon

Collects multiple quality metrics from a bam file

Input

01201010

Output

mq_metrics qd_metrics gc_summary gc_metrics aln_metrics is_metrics mq_plot qd_plot is_plot gc_plot versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_dedup

mem dedup map bam cram sentieon

Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.

Input

0120101

Output

cram crai bam bai score metrics metrics_multiqc_tsv versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_dnamodelapply

dnamodelapply vcf filter sentieon

modifies the input VCF file by adding the MLrejected FILTER to the variants

Input

012010101

Output

vcf index versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_dnascope

dnascope sentieon variant_calling

DNAscope algorithm performs an improved version of Haplotype variant calling.

Input

01230101010101000

Output

vcf vcf_tbi gvcf gvcf_tbi versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

SENTIEON_GVCFTYPER

joint genotyping genotype gvcf

Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.

Input

012301010101

Output

vcf_gz vcf_gz_tbi versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_haplotyper

sentieon haplotypecaller haplotype

Runs Sentieon's haplotyper for germline variant calling.

Input

012340101010100

Output

vcf vcf_tbi gvcf gvcf_tbi versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_qualcal

base quality score recalibration bqsr sentieon

Generate recalibration table and optionally perform base quality recalibration

Input

01201010101010

Output

table table_post recal_alignment csv pdf versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_readwriter

merge convert readwriter sentieon

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

Input

0120101

Output

output index output_index versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_tnfilter

tnfilter filter sentieon tnhaplotyper2 vcf

Filters the raw output of sentieon/tnhaplotyper2.

Input

01234560101

Output

vcf vcf_tbi stats versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_tnhaplotyper2

tnseq tnhaplotyper2 sentieon variant_calling

Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.

Input

01230101010101010100

Output

orientation_data contamination_data contamination_segments stats vcf index versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_tnscope

tnscope sentieon variant_calling

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

Input

012010101201201201

Output

vcf index versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_varcal

sentieon varcal variant recalibration

Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm

Input

01200000

Output

recal idx tranches plots versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon_wgsmetrics

metrics bam sentieon

Collects whole genome quality metrics from a bam file

Input

012010101

Output

wgs_metrics versions

Tools

sentieon:

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

seqcluster_collapse

smrnaseq cluster mirna

Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.

Input

01

Output

fastq versions

Tools

seqcluster:

Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.

seqfu_derep

dereplicate fasta uniques

Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers.

Input

01

Output

fasta versions

Tools

seqfu:

DNA sequence utilities for FASTX files

seqfu_stats

seqfu stats n50

Statistics for FASTA or FASTQ files

Input

01

Output

stats multiqc versions

Tools

seqfu:

Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files

seqkit_concat

concat fasta fastq merge

Concatenating multiple uncompressed sequence files together

Input

01

Output

fastx versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_fq2fa

fastq fasta convert

Convert FASTQ to FASTA format

Input

01

Output

fasta versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_fx2tab

fasta fastq text tabular convert

Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.

Input

01

Output

text versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_grep

filter seqkit subseq grep

Select sequences from a large file based on name/ID

Input

010

Output

filter versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_pair

seqkit pair fastq

match up paired-end reads from two fastq files

Input

01

Output

reads unpaired_reads versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_replace

seqkit replace sequence sequence headers fasta

Use seqkit to find/replace strings within sequences and sequence headers

Input

01

Output

fastx versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_rmdup

genomics fasta fastq remove duplicates

Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)

Input

01

Output

fastx log versions

Tools

seqkit:

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

seqkit_seq

genomics fasta fastq transform filter gaps complement

Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)

Input

01

Output

fastx versions

Tools

seqkit:

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

seqkit_sliding

seqkit sliding windows

Use seqkit to generate sliding windows of input fasta

Input

01

Output

fastx versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_sort

genomics fasta fastq sort

Sorts sequences by id/name/sequence/length

Input

01

Output

fastx versions

Tools

seqkit:

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

seqkit_split2

split fastq seqkit

Split single or paired-end fastq.gz files

Input

01

Output

reads versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_stats

seqkit fasta stats

simple statistics of FASTA/Q files

Input

01

Output

stats versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_tab2fx

fasta fastq text tabular convert

Convert tabular format (first two/three columns) to FASTA/Q format.

Input

01

Output

fastx versions

Tools

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

seqkit_translate

seqkit translate protein

Translate DNA/RNA to protein sequence

Input

01

Output

fastx versions

Tools

quality_control qc preprocessing

Sequence quality metrics for FASTQ and uBAM files.

Input

01

Output

json html versions

sequencetools_pileupcaller

genotyping mpileup random draw pseudohaploid pseudodiploid freqsum plink bed eigenstrat

PileupCaller is a tool to create genotype calls from bam files using read-sampling methods

Input

0100

Output

eigenstrat plink freqsum versions

Tools

sequencetools:

Tools for population genetics on sequencing data

sequenzautils_bam2seqz

sequenzautils copy number bam2seqz

Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file

Input

01200

Output

seqz versions

Tools

sequenzautils:

Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.

sequenzautils_gcwiggle

sequenzautils copy number gc_wiggle

Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size.

Input

01

Output

wig versions

Tools

sequenzautils:

Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format.

seqwish_induce

induce paf gfa graph variation graph

Induce a variation graph in GFA format from alignments in PAF format

Input

012

Output

gfa versions

Tools

seqwish:

seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.

seroba_run

fastq serotype Streptococcus pneumoniae

Determine Streptococcus pneumoniae serotype from Illumina paired-end reads

Input

01

Output

tsv txt versions

Tools

seroba:

SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.

severus

structural variation somatic germline long-read

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)

Input

01234501

Output

log read_qual breakpoints_double read_alignments read_ids collapsed_dup loh all_vcf all_breakpoints_clusters_list all_breakpoints_clusters all_plots somatic_vcf somatic_breakpoints_clusters_list somatic_breakpoints_clusters somatic_plots versions

sexdeterrmine

sex determination genetic sex relative coverage ancient dna

Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.

Input

010

nanopore de-novo assembly longread

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.

Input

01

Output

assembly gfa results versions

shasum

checksum sha256 256 bit

Print SHA256 (256-bit) checksums.

Input

01

Output

checksum versions

Tools

md5sum:

Create an SHA256 (256-bit) checksum.

shigatyper

fastq shigella serotype

Determine Shigella serotype from Illumina or Oxford Nanopore reads

Input

01

bacterial assembly illumina

Assemble bacterial isolate genomes from Illumina paired-end reads

Input

01

FASTQ compression lossless

Fast, efficient, lossless compression of FASTQ files.

Input

01

Output

sfq versions

smncopynumbercaller

copy number BAM CRAM SMN1 SMN2

tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.

Input

012

Output

smncopynumber run_metrics versions

smoothxg

gfa graph pangenome variation graph POA

Linearize and simplify variation graph in GFA format using blocked partial order alignment

Input

01

Output

gfa maf versions

smoove_call

structural variants SV vcf wgs

smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.

Input

01230101

Output

vcf versions

Tools

sniffles structural-variant calling long-read

structural-variant calling with sniffles

Input

012010100

Output

vcf tbi snf versions

snippy_core

core alignment bacteria snippy

Core-SNP alignment from Snippy outputs

Input

0120

Output

aln full_aln tab vcf txt versions

Tools

snippy:

Rapid bacterial SNP calling and core genome alignments

snippy_run

variant fastq bacteria

Rapid haploid variant calling

Input

010

Output

tab csv html vcf bed gff bam bai log aligned_fa consensus_fa consensus_subs_fa raw_vcf filt_vcf vcf_gz vcf_csi txt versions

Tools

SNPs invariant constant

Rapidly extracts SNPs from a multi-FASTA alignment.

Input

0

Output

fasta constant_sites versions constant_sites_string

somalier_ancestry

relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Input

01012

Output

tsv html versions

Tools

somalier:

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

somalier_extract

relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Input

012010101

Output

extract versions

Tools

somalier:

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

somalier_relate

relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Input

0120

Output

html pairs_tsv samples_tsv versions

Tools

somalier:

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

sortmerna

filtering mapping clustering rRNA ribosomal RNA

Local sequence alignment tool for filtering, mapping and clustering.

Input

010101

Output

reads log index versions

Tools

genome assembly genome assembler small genome de novo assembler

Assembles a small genome (bacterial, fungal, viral)

Input

012300

Output

scaffolds contigs transcripts gene_clusters gfa warnings log versions

spatyper

fasta spatype spa

Computational method for finding spa types.

Input

0100

Output

tsv versions

splitubam

long-read bam genomics

split one ubam into multiple, per line, fast

Input

01

bacteria fasta streptococcus

Serotype prediction of Streptococcus suis assemblies

Input

01

Output

tsv versions

stadeniolib_scramble

sam bam cram compression

Advanced sequence file format conversions

Input

01000

Output

cram gzi versions

Tools

stardist segmentation image

Cell and nuclear segmentation with star-convex shapes

Input

01

Output

mask versions

starsolo

align count genome reference

Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information.

Input

012001

Output

counts log_final log_out log_progress summary versions

stecfinder

serotype Escherichia coli fastq fasta

Serotype STEC samples from paired-end reads or assemblies

Input

01

Output

tsv versions

stitch

imputation genomics vcf bgen cram bam sam

STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.

Input

0123456789100120

sv structural variants detecting svs short-read sequencing

SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements

Input

01234010101010101

Output

sv indel germ_indel germ_sv som_indel som_sv unfiltered_sv unfiltered_indel unfiltered_germ_indel unfiltered_germ_sv unfiltered_som_indel unfiltered_som_sv raw_calls discordants log versions

svanalyzer_svbenchmark

structural variant sv benchmarking

SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.

Input

0123450101

Output

fns fps distances log report versions

Tools

svanalyzer:

SVanalyzer: tools for the analysis of structural variation in genomes

svdb_build

structural variants build svdb

Build a structural variant database

Input

010

Output

db versions

Tools

svdb:

structural variant database software

svdb_merge

structural variants vcf merge

The merge module merges structural variants within one or more vcf files.

Input

0100

Output

vcf tbi csi versions

Tools

svdb:

structural variant database software

svdb_query

structural variants query svdb

Query a structural variant database, using a vcf file as query

Input

01000000

Output

vcf versions

Tools

svdb:

structural variant database software

svtk_baftest

svtk svtk/baftest baftest baf bed structural variants

Performs tests on BAF files

Input

01234

Output

metrics versions

Tools

svtk:

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtk_countsvtypes

svtk countsvtypes vcf structural variants

Count the instances of each SVTYPE observed in each sample in a VCF.

Input

01

Output

counts versions

Tools

svtk:

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtk_rdtest2vcf

svtk rdtest2vcf bed rdtest vcf

Convert an RdTest-formatted bed to the standard VCF format.

Input

0120

Output

vcf tbi versions

Tools

svtk:

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtk_standardize

svtk structural variants SV vcf standardization

Convert SV calls to a standardized format.

Input

010

Output

standardized_vcf versions

Tools

svtk:

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtk_vcf2bed

vcf bed vcf2bed svtk structural variants

Converts VCFs containing structural variants to BED format

Input

012

Output

bed versions

Tools

svtk:

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtools_vcftobedpe

structural bedpe vcf conversion variants

Convert a VCF file to a BEDPE file.

Input

01

Output

bedpe versions

Tools

svtools:

Tools for processing and analyzing structural variants

svtyper_svtyper

sv structural variants genotyping

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data

Input

01230101

Output

json gt_vcf bam versions

Tools

svtyper:

Compute genotype of structural variants based on breakpoint depth

svtyper_svtypersso

sv structural variants genotyping Bayesian

SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample

Input

012301

Output

gt_vcf json versions

Tools

long-read bam genomics

A tool for tagging BAM files.

Input

01

Output

bam versions

tailfindr

polya tail fast5 nanopore

Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA

Input

01

alignment MSA genomics

Aligns sequences using T_COFFEE

Input

01010120

Output

alignment lib versions

Tools

tcoffee:

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.

pigz:

Parallel implementation of the gzip algorithm.

tcoffee_alncompare

alignment MSA evaluation

Compares 2 alternative MSAs to evaluate them.

Input

012

Output

scores versions

Tools

tcoffee:

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

pigz:

Parallel implementation of the gzip algorithm.

tcoffee_consensus

alignment MSA genomics

Computes a consensus alignment using T_COFFEE

Input

01010

Output

alignment eval versions

Tools

tcoffee:

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.

pigz:

reformatting alignment genomics

Reformats files with t-coffee

Input

01

Output

formatted_file versions

Tools

tcoffee:

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.

tcoffee_tcs

alignment MSA evaluation

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

Input

0101

Output

tcs scores versions

Tools

tcoffee:

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

pigz:

Parallel implementation of the gzip algorithm.

telseq

bam cram genomics samtools telomere telseq

Telseq: a software for calculating telomere length

Input

012010101

Output

output versions

Tools

nanopore sequencing quality control genomics

A post sequencing QC tool for Oxford Nanopore sequencers

Input

01

Output

report_data report_html plots_html plotly_js versions

transdecoder_longorf

eucaryotes gff transcript coding

TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.

Input

01

Output

pep gff3 cds dat folder versions

Tools

transdecoder:

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

transdecoder_predict

eukaryotes gff cds transcroder

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

Input

010

Output

pep gff3 cds bed versions

Tools

transdecoder:

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

trgt_genotype

repeat expansion pacbio genomics

Tandem repeat genotyping from PacBio HiFi data

Input

0123010101

Output

vcf bam versions

Tools

trgt:

Tandem repeat genotyping and visualization from PacBio HiFi data

trgt_merge

trgt repeat expansion pacbio genomics

Merge TRGT VCFs from multiple samples

Input

0120101

Output

vcf versions

Tools

trgt:

Tandem repeat genotyping and visualization from PacBio HiFi data

trgt_plot

trgt repeat expansion plotting pacbio genomics

Visualize tandem repeats genotyped by TRGT

Input

012345010101

Output

plot versions

Tools

trgt:

Tandem repeat genotyping and visualization from PacBio HiFi data

trimgalore

trimming adapters sequencing adapters fastq

Trim FastQ files using Trim Galore!

Input

01

Output

reads log unpaired html zip versions

trimmomatic

trimming adapter trimming quality trimming

Performs quality and adapter trimming on paired end and single end reads

Input

01

Output

trimmed_reads unpaired_reads trim_log out_log summary versions

trinity

assembly de novo assembler fasta fastq

Assembles a de novo transcriptome from RNAseq reads

Input

01

genomics transcript selector gene prediction evidence

Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support

Input

01000

Output

tsebra_gtf tsebra_scores versions

tximeta_tximport

gene kallisto pseudoalignment salmon transcript

Import transcript-level abundances and estimated counts for gene-level analysis packages

Input

01010

Output

tpm_gene counts_gene counts_gene_length_scaled counts_gene_scaled lengths_gene tpm_transcript counts_transcript lengths_transcript versions

Tools

tximeta:

Transcript Quantification Import with Automatic Metadata

ucsc_bedclip

bed genomics ucsc

Remove lines from bed file that refer to off-chromosome locations.

Input

010

Output

bedgraph versions

Tools

ucsc:

Remove lines from bed file that refer to off-chromosome locations.

ucsc_bedgraphtobigwig

bedgraph bigwig ucsc bedgraphtobigwig converter

Convert a bedGraph file to bigWig format.

Input

010

Output

bigwig versions

Tools

ucsc:

Convert a bedGraph file to bigWig format.

ucsc_bedtobigbed

bed bigbed ucsc bedtobigbed converter

Convert file from bed to bigBed format

Input

0100

Output

bigbed versions

Tools

ucsc:

Convert file from bed to bigBed format

ucsc_bigwigaverageoverbed

bigwig bedGraph ucsc

compute average score of bigwig over bed file

Input

010

Output

tab versions

Tools

ucsc:

Compute average score of big wig over each bed, which may have introns.

ucsc_gtftogenepred

gtf genepred refflat ucsc gtftogenepred

compute average score of bigwig over bed file

Input

01

Output

genepred refflat versions

Tools

ucsc:

Convert GTF files to GenePred format

ucsc_liftover

bed ucsc ucsc/liftover

convert between genome builds

Input

010

Output

lifted unlifted versions

Tools

ucsc:

Move annotations from one assembly to another

ucsc_wigtobigwig

wig bigwig ucsc

Convert ascii format wig file to binary big wig format

Input

010

Output

bw versions

Tools

ucsc:

Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format

ultra_align

uLTRA align minimap2 long_read isoseq ont

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome

Input

01001

Output

bam versions

Tools

ultra:

Splice aligner of long transcriptomic reads to genome.

ultra_index

uLTRA index minimap2 long_read isoseq ont

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment

Input

00

Output

index versions

Tools

ultra:

Splice aligner of long transcriptomic reads to genome.

ultra_pipeline

uLTRA index minimap2 long_read isoseq ont

uLTRA aligner - A wrapper around minimap2 to improve small exon detection

Input

0100

Output

sam versions

Tools

ultra:

Splice aligner of long transcriptomic reads to genome.

ultraplex

demultiplex fastq umi

Ultraplex is an all-in-one software package for processing and demultiplexing fastq files.

Input

010

genome assembly genome assembler small genome

Assembles bacterial genomes

Input

012

Output

scaffolds gfa log versions

universc

demultiplex align single-cell scRNA-Seq count umi

Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data

Input

010

Output

outs versions

untar

untar uncompress extract

Extract files.

Input

01

Output

untar versions

untarfiles

untar uncompress files

Extract files.

Input

01

Output

files versions

Tools

untar:

Extract tar.gz files.

unzip

unzip decompression zip archiving

Unzip ZIP archive files

Input

01

Output

unzipped_archive versions

unzipfiles

unzip decompression zip archiving

Unzip ZIP archive files

Input

01

Output

files versions

Tools

unzip:

p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.

upd

upd uniparental disomy

Simple software to call UPD regions from germline exome/wgs trios.

Input

01

Output

bed versions

upp_align

alignment MSA genomics structure

Aligns protein structures using UPP

Input

01010

Output

alignment versions

Tools

upp:

SATe-enabled phylogenetic placement

vardictjava

variant calling vcf bam snv sv

The Java port of the VarDict variant caller

Input

01230101

structural_variants array_cgh vcf cytosure

Convert VCF with structural variations to CytoSure format

Input

010101010

Output

cgh versions

vcf2db

vcf2db vcf gemini

A tool to create a Gemini-compatible DB file from an annotated VCF

Input

012

Output

db versions

vcf2maf

vcf maf annotation

vcf2maf

Input

0100

VCFtools VCF sort

A set of tools written in Perl and C++ for working with VCF files

Input

0100

Output

vcf bcf frq frq_count idepth ldepth ldepth_mean gdepth hap_ld geno_ld geno_chisq list_hap_ld list_geno_ld interchrom_hap_ld interchrom_geno_ld tstv tstv_summary tstv_count tstv_qual filter_summary sites_pi windowed_pi weir_fst heterozygosity hwe tajima_d freq_burden lroh relatedness relatedness2 lqual missing_individual missing_site snp_density kept_sites removed_sites singeltons indel_hist hapcount mendel format info genotypes_matrix genotypes_matrix_individual genotypes_matrix_position impute_hap impute_hap_legend impute_hap_indv ldhat_sites ldhat_locs beagle_gl beagle_pl ped map_ tped tfam diff_sites_in_files diff_indv_in_files diff_sites diff_indv diff_discd_matrix diff_switch_error versions

velocyto

count rnaseq rna velocity bam

Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use Path(resolve_path=True) and breaks the nextflow logic of symbolic links. If in the work dir velocyto find a file named EXACTLY cellsorted_[ORIGINAL_BAM_NAME] it will skip the samtools sort step. Cellsorted bam file should be cell sorted with:

    samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam

See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:

    withName: SAMTOOLS_SORT {
        ext.prefix = { "cellsorted_${bam.baseName}" }
        ext.args = '-t CB -O BAM'
    }

Optional mask must be passed with ext.args and option --mask This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also velocyto tutorial

Input

01230

Output

loom versions

VERIFYBAMID_VERIFYBAMID

qc contamination bam

Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.

Input

0120

Output

log selfsm depthsm selfrg depthrg bestsm bestrg versions

Tools

verifybamid:

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.

VERIFYBAMID_VERIFYBAMID2

contamination bam verifybamid DNA contamination estimation

Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.

Input

01201200

Output

log ud bed mu self_sm ancestry versions

Tools

verifybamid2:

A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

vg_construct

vg graph construct fasta vcf structural variants

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

Input

01230101

Output

graph versions

Tools

vg:

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

vg_deconstruct

vcf gfa graph pangenome graph variation graph graph projection to vcf

Deconstruct snarls present in a variation graph in GFA format to variants in VCF format

Input

0100

Output

vcf versions

Tools

vg:

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

long read alignment pangenome-scale all versus all mashmap wavefront

a pangenome-scale aligner

Input

0123400

Output

paf versions

wgsim

simulate fasta reads

simulating sequence reads from a reference genome

Input

01

structural-variants benchmarking vcf

A large variant benchmarking tool analogous to hap.py for small variants.

Input

01234

Output

report bench_vcf bench_vcf_tbi versions

xengsort_index

index QC reference fasta xenograft sort k-mer

Fast lightweight accurate xenograft sorting

Input

00000

Output

hash info versions

Tools

xengsort:

A fast xenograft read sorter based on space-efficient k-mer hashing

xeniumranger_import_segmentation

spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging

The xeniumranger import-segmentation module allows you to specify 2D nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation results can be generated by community-developed tools or prior Xenium segmentation result.

Input

01000000

Output

outs versions

Tools

xeniumranger:

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.

xeniumranger_relabel

spatial relabel gene labels transcripts xeniumranger

The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.

Input

010

Output

outs versions

Tools

xeniumranger:

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.

xeniumranger_rename

spatial rename gene labels transcripts xeniumranger

The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.

Input

0100

Output

outs versions

Tools

xeniumranger:

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.

xeniumranger_resegment

spatial resegment morphology segmentation xeniumranger

The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.

Input

010000

Output

outs versions

Tools

xeniumranger:

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.

xz_compress

xz compression archive

Compresses files with xz.

Input

01

Output

archive versions

Tools

xz:

xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2.

xz_decompress

xz decompression compression

Decompresses files with xz.

Input

01

Output

file versions

Tools

unzip decompression zip archiving

Compress file lists to produce ZIP archive files

Input

01

Output

zipped_archive versions

Tools

unzip:

p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.

Available Modules