Modules

Input

metareadsadapterlist

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

metafastq

fasta virulence Staphylococcus aureus

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

Input

metafasta

Output

meta summary results_dir versions

ale

reference-independent assembly evaluation

ALE: assembly likelihood estimator.

Input

metaasmbam

Output

meta ale versions

allelecounter

allele count coverage

Generates a count of coverage of alleles

Input

metainputinput_indexlocifasta

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

metafaamodelmin_lengthmin_probability

Output

meta versions amps_faa amps_tsv

amplify_predict

antimicrobial peptides AMPs prediction model

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

Input

metafaamodel_dir

Output

meta versions tsv

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

metainput_tsvtooldb

bam copy number cram

copy number profiles of tumour cells.

Input

argsmetainput_normalindex_normalinput_tumorindex_tumorallele_filesloci_filesbed_filefastagc_filert_file

Output

meta allelefreqs metrics png purityploidy segments versions

ashlar

image_processing alignment registration

Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

Input

metaimages

background cycif autofluorescence image_analysis mcmicro highly_multiplexed_imaging

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

Input

metaimagemeta2markerfile

bam clean align

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

Input

metabam

Output

meta versions bam

bamclipper

primer clipping genomics bam

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

Input

metabambaibedpe

Output

meta versions bam bai

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

metaprimary_aligned_bamcontaminant_aligned_bam

Output

versions primary_filtered_bam contamination_bam

bamstats_generalstats

bam statistics genomics

write your description here

Input

metabam

Output

meta versions json

Tools

rrna sequences removal

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

Input

metareadsdbname

Output

meta versions gff

bases2fastq

demultiplex element fastq

Demultiplex Element Biosciences bases files

Input

metarun_manifestrun_dir

demultiplex illumina fastq

Demultiplex Illumina BCL files

Input

metasamplesheetrun_dir

Output

versions fastq fastq_idx undetermined undetermined_idx reports stats interop

bclconvert

demultiplex illumina fastq

Demultiplex Illumina BCL files

Input

metasamplesheetrun_dir

Output

versions fastq fastq_idx undetermined undetermined_idx reports logs interop

beagle5_beagle

phasing imputation

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

Input

metavcfrefgenmapexclsamplesexclmarkers

Output

meta versions vcf log

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

metainput

Output

meta versions output

biobambam_bammarkduplicates2

markduplicates bam cram

Locate and tag duplicate reads in a BAM file

Input

metabam

Output

meta bam metrics versions

Tools

biobambam:

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

biobambam_bammerge

merge bam

Merge a list of sorted bam files

Input

metabam

Output

meta 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

metabamsmeta2fasta

Output

meta 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

metaseqsscheme_metadata

Output

meta versions summary kmer_results simple_summary

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

metareadsindex

Output

meta 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

metareadsindex

Output

meta 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

metabambaiindex

Output

meta bsconv_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

metabambaisnp_bedindex

Output

meta epiread_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

fasta

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

metabedindex

Output

meta mergecg_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

metanormal_bamsnormal_baistumor_bamtumor_baiindex

Output

meta versions vcf

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

metabam

Output

biscuit_qc_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

metavcf

Output

meta 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

metareadsindex

Output

meta bam unmapped 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_coverage2cytosine

bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph

Relates methylation calls back to genomic cytosine contexts.

Input

metacoverage_fileindex

Output

meta 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

metabam

Output

meta 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

fasta

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

metabamindex

Output

meta 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

metaalign_reportsplitting_reportdedup_reportmbiasfasta

Output

meta 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

bamalign_reportdedup_reportsplitting_reportmbias

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

metaentryentry_batchmeta2db

Output

meta 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

metafastameta2db

Output

meta 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

metafastameta2dbout_ext

Output

meta 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

metafasta

Output

meta 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

metafastameta2db

Output

meta txt versions

Tools

blast:

Protein to Translated Nucleotide BLAST.

blast_updateblastdb

fasta blast download database

Downloads a BLAST database from NCBI

Input

metaname

Output

meta 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

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_dir 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

short_summary_txt

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.

bwa_aln

bwa aln short-read align reference fasta map fastq

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

Input

metareadsmeta2index

Output

meta versions sai

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

metafasta

Output

meta 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

metareadsmeta2indexfastasort_bam

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

metareadssaimeta2index

Output

meta versions bam

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

metareadssaimeta2index

Output

meta versions bam

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

metafasta

Output

meta 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

metareadsmeta2indexmeta3fastasort_bam

Output

meta 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

metafasta

Output

meta versions index

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

metareadsmeta2indexmeta3fastasort_bammbuffersort_threads

Output

meta 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

metareadsindex

Output

meta 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

fasta

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

metavcfannotation_dir

Output

meta versions tsv

calder2

calder2 genome topology compartments domains hi-c

Hierarchical Hi-C compartment computation

Input

metainputresolution

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

metaimg_datasignaturehigh_thresholdslow_thresholds

QC Illumina genomics

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

Input

run_dircheckqc_config

Output

versions report

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

versions checkv_db

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

metafastadb

Output

meta versions quality_summary completeness contamination complete_genomes proviruses viruses

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

metafastadb

Output

meta versions checkv_db

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

metafastaprodigal_tfcds

Output

versions meta schema cds_coordinates invalid_cds

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

metafastq

Output

meta versions fastq

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

metareadsmeta2fastameta3indexbarcodeswhitelistchr_orderpairs_chr_order

Output

meta versions bed bam tagAlign pairs

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

metafasta

Output

versions meta index

Tools

sort example genomics

binning of metagenomic sequences

Input

metafasta

Output

meta versions fasta bins fm index links result

clippy

iCLIP eCLIP CLIP

Runs the Clippy CLIP peak caller

Input

metabedgtffai

Output

peaks summits version

clonalframeml

fasta multiple sequence alignment recombination

Predict recomination events in bacterial genomes

Input

metamsanewick

Output

meta versions emsim em fasta newick pos_ref status

clustalo_align

alignment MSA genomics

Align sequences using Clustal Omega

Input

metafastameta2treecompress

Output

meta 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

metafasta

Output

meta 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

metabambaigfffasta

Output

meta versions polymut

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

metafastameta2exclude_bed

Output

meta 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

metatargets

Output

meta 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

metatumornormalmeta2fastameta3fasta_faimeta4targetsmeta5referencepanel_of_normals

Output

meta 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

metacnsvcf

Output

meta versions output

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

metacns

Output

meta versions cns

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

metacnrcns

Output

meta txt 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

fastatargetsantitargets

Output

meta 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

metabaitsmeta2annotation

Output

meta 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

metameta2meta3meta4bambairootfastafai

Output

output_meta versions root tab

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

metacalls

Output

meta versions vcf

Tools

cnvnator:

Tool for calling copy number variations.

cnvpytor_callcnvs

CNV calling

command line tool for calling CNVs in whole genome sequencing data

Input

metapytorbin_sizes

Output

meta pytor versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_histogram

cnv calling histogram

calculates read depth histograms

Input

metapytorbin_sizes

Output

meta pytor versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_importreaddepth

read depth cnv calling

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

Input

metainput_fileindexfastafai

Output

meta pytor versions

Tools

cnvpytor -rd:

calling CNVs using read depth

cnvpytor_partition

cnv calling partition histograms

partitioning read depth histograms

Input

metapytorbin_sizes

Output

meta partitions versions

Tools

cnvpytor:

calling CNVs using read depth

cnvpytor_view

cnv calling

view function to generate vcfs

Input

metapytor_filesbin_sizesoutput_format

Output

meta tsv vcf 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

metafastacoveragequerybamassemblerminkmaxk

Output

meta extended_assemblies extended_circular extended_partial extended_failed orphan_end all_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

metainput

Output

meta 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

metainput

Output

meta 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

metacoverage_filefasta

Output

meta versions args_txt clustering_csv log_txt original_data_csv pca_components_csv pca_transformed_csv

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

metabedbamfilesbaifiles

Output

meta versions tsv

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

metafastabed

Output

meta versions fasta bed

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

metaoriginal_fastacsv

Output

meta versions fasta

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

metaclustering_csv

Output

meta versions csv

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

imagemeta

Output

versions cores masks tma_map centroids meta

crabz_compress

compression gzip zlib

Compress files with crabz

Input

metafile

Output

meta versions archive

Tools

crabz:

Like pigz, but rust

crabz_decompress

decompression gzip zlib

Decompress files with crabz

Input

metaarchive

Output

meta versions file

Tools

crabz:

Like pigz, but rust

crisprcleanr_normalize

sort CNV correction CRISPR

remove false positives of functional crispr genomics due to CNVs

Input

metacount_filelibrary_file

Output

meta versions norm_count_file

Tools

cutesv structural-variant calling

structural-variant calling with cutesv

Input

metabambaimeta2fasta

visualisation tsv csv

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

Input

metaconfig_filetable

Output

versions report

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

metamatnetargs

transmembrane protein classification

A Deep Learning Model for Transmembrane Topology Prediction and Classification

Input

metafasta

Output

meta gff3 line3 md csv png versions

deeptools_bamcoverage

coverage depth track

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

Input

metainputinput_indexfastafasta_fai

Output

meta versions bigWig bedgraph

Tools

deeptools:

A set of user-friendly tools for normalization and visualzation of deep-sequencing data

deeptools_computematrix

genome regions scores matrix

calculates scores per genome regions for other deeptools plotting utilities

Input

metabigwigbed

Output

meta matrix table versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_multibamsummary

bam coverage

Computes read coverage for genomic regions (bins) across the entire genome.

Input

metabambaislabels

Output

meta matrix versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_plotcorrelation

corrrelation matrix heatmap scatterplot

Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.

Input

metamatrixmethodplot_type

Output

meta pdf matrix versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_plotfingerprint

plot fingerprint cumulative coverage bam

plots cumulative reads coverages by BAM file

Input

metabambais

Output

meta pdf matrix metrics versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_plotheatmap

plot heatmap scores matrix

plots values produced by deeptools_computematrix as a heatmap

Input

metamatrix

Output

meta pdf matrix versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_plotpca

PCA matrix

Generates principal component analysis (PCA) plot using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.

Input

metamatrix

Output

meta pdf tab versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools_plotprofile

plot profile scores matrix

plots values produced by deeptools_computematrix as a profile plot

Input

metamatrix

Output

meta pdf matrix versions

Tools

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deepvariant

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

metainputindexintervalmeta2fastameta3faimeta4gzi

Output

meta vcf gvcf version

delly_call

genome structural variants bcf

Call structural variants

Input

metainputinput_indexvcfvcf_indexexclude_bedmeta2fastameta3fai

Output

meta versions bcf csi

Tools

bacterial assembly nanopore

Assemble bacterial isolate genomes from Nanopore reads

Input

metashortreadslongreads

Output

meta versions contigs log raw_contigs txt gfa

dshbio_exportsegments

gfa assembly segment

Export assembly segment sequences in GFA 1.0 format to FASTA format

Input

metagfa

Output

meta fasta versions

Tools

dshbio:

Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.

dshbio_filterbed

bed filter feature

Filter features in gzipped BED format

Input

metabed

Output

meta bed versions

Tools

dshbio:

Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.

dshbio_filtergff3

gff3 filter feature

Filter features in gzipped GFF3 format

Input

metagff3

Output

meta gff3 versions

Tools

dshbio:

Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.

dshbio_splitbed

bed split feature

Split features in gzipped BED format

Input

metabed

Output

meta bed versions

Tools

dshbio:

Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.

dshbio_splitgff3

gff3 split feature

Split features in gzipped GFF3 format

Input

fasta Streptococcus pyogenes typing

EMM typing of Streptococcus pyogenes assemblies

Input

metafasta

site frequency spectrum ancestral alleles derived alleles

estimation of the unfolded site frequency spectrum

Input

metae_configdataseed

Output

meta versions sfs_out pvalues_out

evigene_tr2aacds

genomics transcript assembly clean polish filter redundant duplicate

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

Input

metafasta

Output

meta dropset okayset versions

Tools

trimming quality control fastq faqcs

Perform adapter and quality trimming on sequencing reads with reporting

Input

metareads

Output

meta versions reads reads_fail reads_unpaired stats debug statspdf log

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

metainputhmm_model

Output

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

fastani

genome fasta ANI

Alignment-free computation of average nucleotide Identity (ANI)

Input

metaqueryreference

Output

meta 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

metafasta

Output

meta success_log error_log versions

Tools

phylogenetics newick minimum_evolution distance-based

Distance-based phylogeny with FastME

Input

metainfiletopo

Output

versions nwk stats matrix bootstrap

fastp

trimming quality control fastq

Perform adapter/quality trimming on sequencing reads

Input

metareadsadapter_fastadiscard_trimmed_passsave_trimmed_failsave_merged

Output

meta reads json html log versions reads_fail reads_merged

fastqc

quality control qc adapters fastq

Run FastQC on sequenced reads

Input

metareads

phylogeny newick

Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments.

Input

alignment

Output

versions phylogeny

fastx_collapser

collapse genomics fasta fastq

Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)

Input

metafastx

Output

meta versions fasta

Tools

fastx:

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

fcs_fcsadaptor

assembly genomics quality control contamination NCBI

Run NCBI's FCS adaptor on assembled genomes

Input

metaassembly

Output

meta versions cleaned_assembly adaptor_report log pipeline_args skipped_trims

Tools

fcs:

The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly.

fcs_fcsgx

assembly genomics quality control contamination NCBI

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

Input

metaassemblydatabase

Output

meta versions fcs_gx_report taxonomy_report

Tools

UMIs QC bam duplex

Collects a suite of metrics to QC duplex sequencing data.

Input

metagrouped_baminterval_list

Output

meta versions family_sizes duplex_family_sizes duplex_yield_metrics umi_counts duplex_qc duplex_umi_counts

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

reads

Output

meta version bam cram

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

metabammeta2fastamin_readsmin_baseqmax_base_error_rate

Output

meta 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

metabamstrategy

Output

meta versions bam histogram

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

metabam

Output

meta 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

metamapped_bammeta2unmapped_bammeta3fastameta4dict

Output

meta bam versions

Tools

fgbio:

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

filtlong

nanopore quality control QC filtering long reads short reads

Filtlong filters long reads based on quality measures or short read data.

Input

metashortreadslongreads

Output

meta versions reads log

flash

sort reads merging merge mate pairs

Perform merging of mate paired-end sequencing reads

Input

metareads

demultiplex fastq rust

Demultiplex fastq files

Input

metasample_sheetfastq_readstructure_pairs

genomics cluster genome metagenomics

Cluster genome FASTA files by average nucleotide identity

Input

metabinsqc_tableqc_format

Output

meta tsv dereplicated_bins versions

gamma_gamma

gamma gene-calling

Gene Allele Mutation Microbial Assessment

Input

metafastadb

Output

meta versions gamma psl gff fasta

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

metainputprogram_file

Output

meta versions output

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

metainputhmmmodel_dir

Output

meta versions genes features clusters gbk json

Tools

gecco:

Biosynthetic Gene Cluster prediction with Conditional Random Fields.

gem2_gem2bedmappability

mappability bedgraph index gem

Convert a mappability file to bedgraph format

Input

metamapmeta2index

Output

meta versions bedgraph sizes

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

metafasta

Output

meta versions gem log

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

metaindexread_length

Output

meta versions map

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

metafasta

Output

meta versions gem info

Tools

gem3:

The GEM indexer (v3).

gem3_gem3mapper

fastq genomics mappability

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

Input

metameta2fastqgemsort_bam

Output

meta versions bam

Tools

genome size genome heterozygosity repeat content

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

Input

metahistogram

Output

meta versions linear_plot_png linear_plot_png transformed_linear_plot_png log_plot_png transformed_log_plot_png model summary lookup_table fitted_histogram_png

genotyphi_parse

genotype Salmonella Typhi

Genotype Salmonella Typhi from Mykrobe results

Input

metajson

Output

meta versions tsv

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

metatreatment_bamcontrol_bamblacklist_bedsave_pvaluessave_pileupsave_bedsave_duplicates

gfa graph pangenome variation graph

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

Input

metagfa

transcripts gtf merge compare

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

Input

metagtfsfastafaireference_gtf

merge gvcf

merge gVCF files and perform joint variant calling

Input

metagvcfs

Output

versions bcf

GNU_SORT

GNU sort merge compare

Writes a sorted concatenation of file/s

Input

metainput

Output

meta sorted versions

Tools

sort:

Writes a sorted concatenation of file/s

gnu_split

gnu split coreutils generic

Split a file into consecutive or interleaved sections

Input

metainput

Output

meta split versions

Tools

gnu:

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

goat_taxonsearch

public datasets ncbi genomes on a tree

Query metadata for any taxon across the tree of life.

Input

metataxontaxa_file

Output

meta versions taxonsearch

Tools

goat:

goat-cli is a command line interface to query the Genomes on a Tree Open API.

goleft_indexcov

coverage cnv genomics depth

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

Input

metabamsindexesfai

Output

meta output bams

Tools

goleft:

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

goleft_indexsplit

bam bed cram index split

Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files

Input

metabaimeta2fai

Output

meta bed versions

Tools

goleft:

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

gprofiler2_gost

gene set analysis enrichment gprofiler2 gost gene set

runs a functional enrichment analysis with gprofiler2

Input

metade_filecontrast_variablereferencetargetbackground_filegmt_file

Output

meta all_enrich rds plot_png plot_html sub_enrich sub_plot filtered_gmt session_info versions

Tools

gprofiler2:

An R interface corresponding to the 2019 update of g:Profiler web tool.

grabix_check

compression bgzip grabix

Checks if the input file is bgzip compressed or not

Input

input

Output

versions compress_bgzip

Tools

grabix:

a wee tool for random access into BGZF files.

graphmap2_align

align fasta fastq genome reference

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

metafastqfastaindex

Output

meta sam versions

Tools

graphmap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

graphmap2_index

index fasta reference

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

fasta

Output

gmidx versions

Tools

graphmap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

graphtyper_genotype

variant vcf bam cram pangenome

Tools for population-scale genotyping using pangenome graphs.

Input

metabambairefref_fairegion_file

Output

meta versions vcf tbi

Tools

graphtyper:

A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants.

graphtyper_vcfconcatenate

combine concatenate variant vcf

Tools for population-scale genotyping using pangenome graphs.

Input

metavcf

Output

meta versions vcf tbi

Tools

graphtyper:

A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants.

gridss_gridss

gridss structural variants bam cram vcf

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

metainputsfastafasta_faibwa_index

Output

meta versions vcf

Tools

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gridss_gridssgenerateponbedpe

gridss structural variants bedpe bed vcf

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

metameta2meta3meta4vcfbedpebedfastafasta_faibwa_index

Output

meta versions bedpe bed

Tools

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gridss_gridsssomaticfilter

gridss structural variants somatic variants vcf

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

metameta2vcfpondir

Output

meta versions high_conf_sv all_sv

Tools

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gsea_gsea

gene set analysis enrichment gsea gene set

run the Broad Gene Set Enrichment tool in GSEA mode

Input

metagctclsgene_setsreferencetargetchip

Output

meta rpt index_html heat_map_corr_plot report_tsvs_ref report_htmls_ref report_tsvs_target report_htmls_target ranked_gene_list gene_set_sizes butterfly_plot histogram heatmap pvalues_vs_nes_plot ranked_list_corr gene_set_tsv gene_set_html gene_set_heatmap snapshot gene_set_enplot gene_set_dist archive versions

Tools

gsea:

Gene Set Enrichment Analysis (GSEA)

GSTAMA_COLLAPSE

tama_collapse.py isoseq nanopore long-read transcriptome gene model TAMA

Collapse redundant transcript models in Iso-Seq data.

Input

metabamfasta

Output

meta versions bed bed_trans_reads local_density_error polya read strand_check trans_report varcov variants

Tools

tama_collapse.py:

Collapse similar gene model

gstama_merge

gstama gstama/merge long-read isoseq nanopore tama trancriptome annotation

Merge multiple transcriptomes while maintaining source information.

Input

metabed

Output

meta bed gene_report merge trans_report versions

Tools

gstama:

Gene-Switch Transcriptome Annotation by Modular Algorithms

gstama_polyacleanup

gstama gstama/polyacleanup long-read isoseq tama trancriptome annotation

Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)

Input

metafasta

Output

meta versions fasta report tails

Tools

gstama:

Gene-Switch Transcriptome Annotation by Modular Algorithms

gt_gff3

genome gff3 annotation

GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files

Input

metagff3

Output

meta gt_gff3 error_log versions

Tools

gt:

The GenomeTools genome analysis system

gt_gff3validator

genome gff3 annotation validation

GenomeTools gt-gff3validator utility to strictly validate a GFF3 file

Input

metagff3

Output

meta success_log error_log versions

Tools

gt:

The GenomeTools genome analysis system

gt_ltrharvest

genomics genome annotation repeat transposons retrotransposons

Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility

Input

metaindex

Output

meta tabout gff3 fasta inner_fasta versions

Tools

gt:

The GenomeTools genome analysis system

gt_stat

genome gff3 annotation statistics stats

GenomeTools gt-stat utility to show statistics about features contained in GFF3 files

Input

metagff3

Output

meta stats versions

Tools

gt:

The GenomeTools genome analysis system

gt_suffixerator

genomics genome fasta index

Computes enhanced suffix array using GenomeTools gt-suffixerator utility

Input

metafastamode

Output

meta index versions

Tools

gt:

The GenomeTools genome analysis system

gtdbtk_classifywf

GTDB taxonomy taxonomic classification metagenomics classification genome taxonomy database bacteria archaea

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.

Input

metabinsdatabasemash_db

Output

meta versions summary tree markers msa user_msa filtered log warnings failed

Tools

gtdbtk:

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.

gtfsort

sort example genomics

Sort GTF files in chr/pos/feature order

Input

gtf

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

metavcfmapexclude

fasta serotype Haemophilus influenzae

Identify cap locus serotype and structure in your Haemophilus influenzae assemblies

Input

metafastadatabase_dirmodel_fp

Output

meta versions gbk svg tsv

hicexplorer_hicpca

eigenvectors PCA hicPCA

Computes PCA eigenvectors for a Hi-C matrix.

Input

metamatrix

Output

meta versions results pca1 pca2

Tools

peaks bed bam sam

Create a tag directory with the HOMER suite

Input

metabamfasta

Output

meta 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

metatagDir

Output

meta 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

Coverting from HOMER peak to BED file formats

Input

metatagDir

Output

meta bed 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

metareadsmeta2umis

demultiplex lexogen fastq

Demultiplex paired-end FASTQ files from QuantSeq-Pool

Input

metareadssamplesheet

Output

versions fastq undetermined stats

idr

IDR peaks ChIP-seq ATAC-seq

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

Input

peakspeak_typeprefix

Output

versions idr log png

igv_js

igv igv.js js genome browser

igv.js is an embeddable interactive genome visualization component

Input

metaalignmentindex

Output

meta browser align_files index_files versions

Tools

annotation fasta protein dna interproscan

Produces protein annotations and predictions from an amino acids FASTA file

Input

metafastainterproscan_database

Output

tsv xml gff3 json versions

iphop_download

metagenomics iphop database download phage bacteria host

Download, extract, and check md5 of iPHoP databases

Input

NO input

Output

iphop_db versions

Tools

iphop:

Predict host genus from genomes of uncultivated phages.

iphop_predict

metagenomics iphop database download phage bacteria host

Predict phage host using iPHoP

Input

metafastaiphop_db

Output

meta versions iphop_genus iphop_genome iphop_detailed_output

Tools

iphop:

Predict host genus from genomes of uncultivated phages.

iqtree

phylogeny newick maximum likelihood

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

Input

metaalignmenttreetree_telmclustmdefpartitions_equalpartitions_proportionalpartitions_unlinkedguide_treesitefreq_inconstraint_treetrees_zsuptreetrees_rf

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

islandpath

genomes genomic islands prediction

Genomic island prediction in bacterial and archaeal genomes

Input

metagenome

jasminesv jasmine structural variants vcf bam

Jointly Accurate Sv Merging with Intersample Network Edges

Input

metavcfsbamssample_distsmeta2fastameta3fasta_faichr_norm

Output

meta versions vcf

jupyternotebook

Python Jupyter jupytext papermill notebook reports

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

Input

metanotebookparametersinput_files

Output

meta report versions

Tools

jupytext:

Jupyter notebooks as plain text scripts or markdown documents

papermill:

Parameterize, execute, and analyze notebooks

nbconvert:

Parameterize, execute, and analyze notebooks

kaiju_kaiju

classify metagenomics fastq taxonomic profiling

Taxonomic classification of metagenomic sequence data using a protein reference database

Input

metareadsdb

Output

meta versions results

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

metatsv

Output

meta versions txt

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kaiju_kaiju2table

classify metagenomics taxonomic profiling

write your description here

Input

metaresultstaxon_rank

Output

meta versions results

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

metakaijukrakendb

Output

meta 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

metafasta

Output

meta versions fmi

Tools

kaiju:

Fast and sensitive taxonomic classification for metagenomics

kalign_align

alignment MSA genomics

Aligns sequences using kalign

Input

metafastacompress

Output

meta alignment versions

Tools

kalign:

Kalign is a fast and accurate multiple sequence alignment algorithm.

kallisto_index

kallisto kallisto/index index

Create kallisto index

Input

metafasta

Output

meta 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

metareadsindexgtfchromosomesfragment_lengthfragment_length_sd

Output

meta versions log abundance abundance_hdf5 run_info

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

metareadsindext2gt1ct2cworkflow_modetechnology

Output

meta count versions

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

fastagtfworkflow_mode

Output

versions kb_ref_idx 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

metareads

Output

meta versions hist json png ps pdf jellyfish_hash

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

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

pe_readsse_readsname

Output

versions reads

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

fastakmer_size

Output

report kmers versions

Tools

fasta kegg kofamscan

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

Input

metafastaprofilesko_list

Output

txt tsv versions

kraken2_add

metagenomics db classification build kraken2 add

Adds fasta files to a Kraken2 taxonomic database

Input

metafastataxonomy_namestaxonomy_nodesaccession2taxid

Output

meta 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

metadbcleaning

Output

meta 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

metareadsdbsave_output_fastqssave_reads_assignment

Output

meta 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

metakreports

Output

meta versions txt

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

metataxidclassified_reads_assignmentclassified_reads_fastqreport

Output

meta 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

metakreport

Output

meta versions krona

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

metacustom_library_dircustom_taxonomy_dir

Output

meta versions db

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

metapattern

Output

meta versions output

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

metasequencessequence_typedbram_chunk_sizesave_output_readsreport_filesave_output

Output

meta 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

versions db

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

metadatabasereport

Output

versions html

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

metareport

Output

meta versions html

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

versions db

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

metamafformatannot_aannot_b

Output

meta png gif 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

metafastxparam_fileindex

Output

meta versions maf multiqc

Tools

last:

LAST finds & aligns related regions of sequences.

last_lastdb

LAST index fasta fastq

Prepare sequences for subsequent alignment with lastal.

Input

metafastx

Output

meta versions index

Tools

last:

LAST finds & aligns related regions of sequences.

last_mafconvert

LAST convert alignment MAF

Converts MAF alignments in another format.

Input

metamafformat

Output

meta versions axt_gz blast_gz blasttab_gz chain_gz gff_gz html_gz psl_gz sam_gz tab_gz

Tools

last:

LAST finds & aligns related regions of sequences.

last_mafswap

LAST reorder alignment MAF

Reorder alignments in a MAF file

Input

metamaf

Output

meta versions maf

Tools

last:

LAST finds & aligns related regions of sequences.

last_postmask

LAST mask alignment MAF

Post-alignment masking

Input

metamaf

Output

meta versions maf

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

metamaf

Output

meta versions maf multiqc

Tools

last:

LAST finds & aligns related regions of sequences.

last_train

LAST train fastq fasta

Find suitable score parameters for sequence alignment

Input

metafastxindex

Output

meta versions param_file multiqc

Tools

last:

LAST finds & aligns related regions of sequences.

learnmsa_align

alignment MSA genomics

Align sequences using learnMSA

Input

metafastacompress

Output

meta 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

metareads

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

metatarget_faref_faref_annotationref_db

Output

meta gff3 polished_gff3 unmapped_txt versions

lima

isoseq ccs primer pacbio barcode

lima - The PacBio Barcode Demultiplexer and Primer Remover

Input

metaccsprimers

Output

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

limma_differential

differential expression microarray limma

runs a differential expression analysis with Limma

Input

metacontrast_variablereferencetargetmeta2samplesheeetintensities

Output

results md_plot rdata model session_info 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

metafasta

Output

meta 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

metafasta

Output

meta versions gff3 scn

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

metafastapass_listannotation_outmonoploid_seqs

Output

meta 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

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

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

metafasta

Output

meta versions amp_prediction smorfs all_orfs readme_file log_file

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

metaipbamcontrolbammacs2_gsize

Output

versions peak xls 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

metaipbamcontrolbammacs3_gsize

Output

meta versions peak xls gapped bed bdg

Tools

macs3:

Model Based Analysis for ChIP-Seq data

mafft

fasta msa multiple sequence alignment

Multiple sequence alignment using MAFFT

Input

metafastameta2addmeta3addfragmentsmeta4addfullmeta5addprofilemeta6addlongcompress

Output

meta versions fas

Tools

pigz:

Parallel implementation of the gzip algorithm.

mageck_count

sort functional genomics sgRNA CRISPR-Cas9

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

Input

metalibraryinputfile

Output

meta versions norm count

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

metacount_tabledesign_matrix

Output

meta versions gene_summary sgrna_summary

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

metacount_table

Output

meta versions gene_summary sgrna_summary r_script

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

metameta2fastatreecompress

Output

meta versions alignment

Tools

magus:

Multiple Sequence Alignment using Graph Clustering

magus_guidetree

MSA guidetree genomics graph

Multiple Sequence Alignment using Graph Clustering

Input

metafasta

Output

meta versions tree

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

fastasgffmapping_db

Output

versions index 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

metafastqsindex

Output

versions rma6 alignments log

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

metabamfasta

Output

meta versions runtime_log fragmisincorporation_plot length_plot misincorporation pctot_freq pgtoa_freq dnacomp lgdistribution 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 fasta folder

mash_dist

mash/dist

Calculate Mash distances between reference and query seqeunces

Input

metareferencequery

Output

meta versions dist

Tools

mash:

Fast sequence distance estimator that uses MinHash

mash_screen

screen containment contamination taxonomic assignment

Screens query sequences against large sequence databases

Input

metaquerysequence_sketch

Output

meta versions screen

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

metareads

Output

meta mash stats versions

Tools

mash:

Fast sequence distance estimator that uses MinHash

mashtree

tree mash fasta fastq

Quickly create a tree using Mash distances

Input

metaseqs

Output

meta versions tree matrix

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

metacontigsreadsabund

Output

meta versions binned_fastas summary log marker unbinned_fasta tooshort_fasta marker_genes

maxquant_lfq

sort

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

fasta Neisseria meningitidis serotype

Serotyping of Neisseria meningitidis assemblies

Input

metafasta

Output

meta versions tsv

merfin_hist

assembly evaluation quality completeness

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

Input

metafasta_assemblymeta1meryl_db_readslookup_tableseqmerspeak

Output

meta versions hist log_stderr

Tools

assembly

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

Input

metareads

microrna mirna target prediction

miRanda is an algorithm for finding genomic targets for microRNAs

Input

metaquerymirbase

Output

meta txt versions

mitohifi_findmitoreference

mitochondrial genome reference genome NCBI

Download a mitochondrial genome to be used as reference for MitoHiFi

Input

species

Output

versions fasta gb

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

inputref_faref_gbinput_modecode

Output

versions fasta 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

metabambaibedmeta2fasta

Output

meta global_txt regions_txt summary_txt per_base_bed per_base_csi per_base_d4 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

motus_downloaddb

Output

versions db

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

inputdbprofile_version_yml

Output

versions txt biom

Tools

motus:

Marker gene-based OTU (mOTU) profiling

motus_profile

classify metagenomics fastq taxonomic profiling

Taxonomic meta-omics profiling using universal marker genes

Input

metareadsdb

Output

meta versions out bam mgc log

Tools

motus:

Marker gene-based OTU (mOTU) profiling

msisensor_msi

homoploymer,microsatellite

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

Input

metanormal_bamnormal_baitumor_bamtumor_baihomopolymers

Output

meta versions txt txt txt txt

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

Scan a reference genome to get microsatellite & homopolymer information

Input

metafasta

Output

meta versions txt

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

msisensor2 detection of MSI regions.

Input

metatumor_bamnormal_bamintervalsmodels

Output

meta 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

msi

msisensor2 detection of MSI regions.

Input

fastaoutput

Output

versions output

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

metanormalnormal_indextumortumor_indexintervalsfastamsisensor_scan

Output

meta output_report output_dis output_germline output_somatic versions list

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

metafasta

Output

meta versions list

Tools

msisensorpro:

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

mtmalign_align

alignment MSA genomics structure

Aligns protein structures using mTM-align

Input

metapdbscompress

Output

meta 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

vcfsfastasnpeff_resultsgffallele_freqsgenotype_qualitycoveragehomozygous_freqheterozygous_freqgff_exclude

Output

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

mummer

align genome fasta

MUMmer is a system for rapidly aligning entire genomes

Input

metarefquery

Output

meta versions coords

muscle

msa multiple sequence alignment

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

fasta

Output

aligned_fasta msf clustalw phyi phys html 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

metafastacompress

Output

meta versions alignment

Tools

muscle -super5:

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

pigz:

Parallel implementation of the gzip algorithm.

mygene

mygene go annotation

Fetch the GO concepts for a list of genes

Input

metagene_list

Output

meta gmt tsv versions

mykrobe_predict

fastq bam antimicrobial resistance

AMR predictions for supported species

Input

metaseqsspecies

Output

meta versions csv json

Tools

mykrobe:

Antibiotic resistance prediction in minutes

nanocomp

bam fasta fastq qc nanopore

Compare multiple runs of long read sequencing data and alignments

Input

metafilelist

Output

versions meta 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

nanofilt

nanopore filtering QC

Filtering and trimming of Oxford Nanopore Sequencing data

Input

metareadssummary_file

Output

meta versions filtreads log_file

nanolyse

contaminant_removal

DNA contaminant removal using NanoLyse

Input

metafastqfasta

Output

meta 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

metabambai

Output

meta 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

metafastqsummary_txt

fasta Neisseria gonorrhoeae serotype

Serotyping Neisseria gonorrhoeae assemblies

Input

metafasta

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 from a single Nonpareil npo file

Input

metanpo

Output

meta versions png

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

metareadsformatmode

Output

meta versions npa npc npl npo

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nonpareil_set

metagenomics statistics coverage complexity redundancy diversity visualisation

Visualise metagenome redundancy curves from multiple Nonpareil npo file in a single image

Input

metanpos

Output

meta versions png

Tools

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

nucmer

align nucleotide

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

Input

metarefquery

cnv bam tumor/normal

Calls CNVs in bam files from tumor patients

Input

metanormalnormal_indextumortumor_indexbedfasta

Output

png profile summary versions

openms_decoydatabase

decoy database openms proteomics fasta

Create a decoy peptide database from a standard FASTA database.

Input

metafasta

Output

meta versions fasta

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

metaid_filefilter_file

Output

meta versions filtered

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

metaidxmls

Output

meta versions idxml

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

metamerged_idxml

Output

meta versions idxmls

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

metaidxml

Output

meta versions idxml

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

metamzml

Output

meta versions mzml

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

metaid_fileid_fasta

Output

meta versions id_file_pi

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

metabambai

Output

meta versions hla_type coverage_plot

orthofinder

genomics orthogroup orthologs gene duplication tree phylogeny

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

Input

metafastas

Output

meta versions orthofinder

paftools_sam2paf

paf bam conversion

A program to convert bam into paf.

Input

metabam

Output

meta paf versions

Tools

sort

Paraclu finds clusters in data attached to sequences.

Input

metabedmin_cluster

Output

meta versions bed

paragraph_idxdepth

bam cram depth paragraph

Determines the depth in a BAM/CRAM file

Input

metameta2meta3inputinput_indexfastafasta_fai

Output

meta versions depth binned_depth

Tools

paragraph:

Graph realignment tools for structural variants

paragraph_multigrmpy

vcf json structural variants graphs genotyping

Genotype structural variants using paragraph and grmpy

Input

metavariantsvariants_indexreadsreads_indexmanifestmeta2fastameta3fasta_fai

Output

meta versions vcf json

Tools

paragraph:

Graph realignment tools for structural variants

paragraph_vcf2paragraph

vcf json structural_variants

Convert a VCF file to a JSON graph

Input

metavcf

Output

meta versions graph

Tools

paragraph:

Graph realignment tools for structural variants

paraphase

paraphase long-read HiFi

HiFi-based caller for highly homologous genes

Input

metabambaimeta2fastameta3config

Output

meta versions bam bai json vcf

pasty

bacteria serogroup fasta assembly

Serogroup Pseudomonas aeruginosa assemblies

Input

metafasta

Output

meta versions tsv blast details

pbbam_pbmerge

pbbam pbbam/pbmerge

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

metabam

Output

meta versions bam pbi

Tools

pbbam:

PacBio BAM C++ library

pbccs

ccs pacbio isoseq subreads

Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads

Input

metabampbichunk_numchunk_on

pair-end read merge

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

Input

metareads

Output

meta versions assembled unassembled discarded

peddy

pedigrees ped family

Manipulation, validation and exploration of pedigrees

Input

metavcfpedvcf_tbi

Output

meta ped html csv png versions

peka

motif CLIP iCLIP genomics k-mer

Runs PEKA CLIP peak k-mer analysis

Input

metapeakscrosslinksfastafaigtf

polishing assembly variant calling

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

Input

metafastameta2bambaipilon_mode

Output

meta versions improved_assembly change_record vcf tracks_bed tracks_wig

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

metabambaibedfastafai

Output

meta versions bp cem del dd int_{final inv li rp si td

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

metabams

Output

meta versions divergent_TREs bidirectional_TREs unidirectional_TREs peakcalling_log

Tools

pints:

Peak Identifier for Nascent Transcripts Starts (PINTS)

pirate

gff pan-genome alignment

Pangenome toolbox for bacterial genomes

Input

metagff

Output

meta versions results aln

plasmidfinder

fasta fastq plasmid

Identify plasmids in bacterial sequences and assemblies

Input

metaseqs

Output

meta versions json txt tsv genome_seq plasmid_seq

plasmidid

assembly plasmid bacterial

assembles bacterial plasmids

Input

metascaffoldfasta

fastq serotype Streptococcus pneumoniae

Determine Streptococcus pneumoniae serotype from Illumina paired-end reads

Input

metareads

Output

meta versions xml txt

popscle_demuxlet

popscle demultiplexing genotype-based deconvoltion single cell

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available.

Input

metaplp_prefixbamdonor_genotype

Output

meta versions demuxlet_result

Tools

popscle:

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

popscle_dscpileup

popscle demultiplexing genotype-based deconvoltion single cell pile up

Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

Input

metabamvcf

Output

meta versions cel plp var umi

Tools

popscle:

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

popscle_freemuxlet

popscle demultiplexing genotype-based deconvoltion single cell

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.

Input

metaplpn_sample

Output

meta versions result vcf lmix singlet_result singlet_vcf

Tools

fasta genome qc nucleotides

Calculate pairwise nucleotide identity with respect to a reference sequence

Input

metafastameta2referencecompress

Output

versions valid_fasta valid_fasta report log

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

metacount

Output

meta propr matrix fdr adj 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

metafasta_files

Output

versions orthologgroups orthologgraph blastgraph

proteus_readproteingroups

proteomics proteus readproteingroups

reads a maxQuant proteinGroups file with Proteus

Input

metasamplesheetintensitiesmeta2contrast_variable

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

metasummary

Output

meta 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

metabambai

Output

meta versions csv

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

metacsv

Output

meta versions csv

Tools

pydamage:

Damage parameter estimation for ancient DNA

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

metafastaoutput_format

quast assembly quality contig scaffold

Quality Assessment Tool for Genome Assemblies

Input

consensusfastagff

Output

quast report misassemblies transcriptome 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

metameta2meta3bamgtffasta

Output

meta best_offset offset offset_plot psites codon_coverage_rpf codon_coverage_psite cds_coverage cds_window_coverage ribowaltz_qc versions

rmarkdownnotebook

R notebook reports

Render an rmarkdown notebook. Supports parametrization.

Input

metanotebookparametersinput_files

Output

meta report 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

metagff

assembly hi-c scaffolding long reads salsa salsa2

SALSA, A tool to scaffold long read assemblies with HiC

Input

metafastaindexbed

Output

meta 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

metabambaidatabase

Output

meta versions csv json bam

Tools

sam2lca:

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

sambamba_flagstat

stats flagstat sambamba

Outputs some statistics drawn from read flags.

Input

metabam

Output

meta versions stats

Tools

sambamba:

Tools for working with SAM/BAM data

sambamba_markdup

markduplicates duplicates bam

find and mark duplicate reads in BAM file

Input

metabam

Output

meta versions bam bai

Tools

cat collate fixmate sort markduplicates bam sam cram multi-tool

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

Input

metainputmeta2fasta

Output

meta 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

metabammeta2fasta

Output

meta 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

metainputinput_indexmeta2fasta

Output

meta 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

metainputindexmeta2fastaqname

Output

meta bam cram sam bai csi crai unselected unselected_index 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.

scimap_mcmicro

sort spatial single cell

SCIMAP is a suite of tools that enables spatial single-cell analyses

Input

metacellByFeature

Output

meta versions annotedDataCsv annotedDataH5ad

Tools

scimap:

Scimap is a scalable toolkit for analyzing spatial molecular data.

scimap_spatiallda

spatial_neighborhoods scimap spatial_omics

SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.

Input

metaphenotyped

Output

meta versions spatial_lda_output composition_plot motif_location_plot

Tools

fasta fastq salmonella sertotype

Salmonella serotype prediction from reads and assemblies

Input

metaseqs

Output

meta versions log tsv txt

seqtk_cutn

cut fasta seqtk

Generates a BED file containing genomic locations of lengths of N.

Input

metafasta

Output

meta bed versions

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.

seqtk_mergepe

interleave merge fastx

Interleave pair-end reads from FastQ files

Input

metareads

Output

meta versions reads

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.

seqtk_rename

rename fastx header

Rename sequence names in FASTQ or FASTA files.

Input

metasequences

Output

meta versions sequences

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.

seqtk_sample

sample fastx reads

Subsample reads from FASTQ files

Input

metareadssample_size

Output

meta versions reads

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.

seqtk_seq

seq filter transformation

Common transformation operations on FASTA or FASTQ files.

Input

metasequences

Output

meta versions sequences

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.

seqtk_subseq

filtering selection fastx

Select only sequences that match the filtering condition

Input

sequencesfilter_list

Output

versions sequences

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

seqtk_trim

trimfq fastq seqtk

Trim low quality bases from FastQ files

Input

metareads

Output

meta versions reads

Tools

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

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

metampileupsnpfilecalling_methodoutput_format

Output

meta versions eigenstrat plink freqsum

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

metanormalbamtumourbamfastawigfile

Output

meta versions seqz

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

metafasta

Output

meta versions wig

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

metapaffasta

Output

meta 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

metareads

Output

meta versions tsv txt

Tools

seroba:

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

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

metadepth

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

metareads

Output

meta versions assembly gfa results

shasum

checksum sha256 256 bit

Print SHA256 (256-bit) checksums.

Input

metafile

Output

meta versions checksum

Tools

md5sum:

Create an SHA256 (256-bit) checksum.

shigatyper

fastq shigella serotype

Determine Shigella serotype from Illumina or Oxford Nanopore reads

Input

metareads

bacterial assembly illumina

Assemble bacterial isolate genomes from Illumina paired-end reads

Input

metareads

bacteria fasta salmonella

Serovar prediction of salmonella assemblies

Input

metafasta

Output

meta versions tsv allele_json allele_fasta cgmlst_csv

slimfastq

FASTQ compression lossless

Fast, efficient, lossless compression of FASTQ files.

Input

metafastq

Output

meta versions sfq

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

bambaimeta

Output

meta run_metrics smncopynumber versions

smoothxg

gfa graph pangenome variation graph POA

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

Input

metagfa

Output

meta gfa versions maf

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. Developped by Brent Pedersen.

Input

metainputindexexclude_bedsfastafai

Output

meta versions vcf

Tools

sniffles structural-variant calling long-read

structural-variant calling with sniffles

Input

metabambaimeta2fasta

Output

meta vcf snf versions

snippy_core

core alignment bacteria snippy

Core-SNP alignment from Snippy outputs

Input

metavcfaligned_fareference

Output

meta versions aln full_aln tab vcf txt

Tools

snippy:

Rapid bacterial SNP calling and core genome alignments

snippy_run

variant fastq bacteria

Rapid haploid variant calling

Input

metareadsindex

Output

meta versions 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

Tools

SNPs invariant constant

Rapidly extracts SNPs from a multi-FASTA alignment.

Input

alignment

Output

versions fasta constant_sites 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

metaquery_somalier_filesmeta2labelled_somalier_fileslabels_tsv

Output

meta versions tsv html

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

metainputinput_indexmeta2fastameta3faimeta4sites

Output

meta versions extract

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

metaextractpedsample_groups

Output

versions html pairs_tsv samples_tsv

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

metareadsmeta2fastasmeta3index

Output

meta reads log meta2 index versions

Tools

SortMeRNA:

The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

sourmash_compare

compare FracMinHash sketch containment sourmash metagenomics genomics kmer

Compare many FracMinHash signatures generated by sourmash sketch.

Input

metasignaturesfile_listsave_numpy_matrixsave_csv

Output

meta versions matrix csv labels

Tools

sourmash:

Compute and compare FracMinHash signatures for DNA and protein data sets.

sourmash_gather

FracMinHash sketch signature kmer containment sourmash genomics metagenomics taxonomic classification taxonomic profiling

Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.

Input

metasignaturedbsave_unassignedsave_matches_sigsave_prefetchsave_prefetch_csv

Output

meta versions result matches unassigned prefetch prefetchcsv

Tools

sourmash:

Compute and compare FracMinHash signatures for DNA data sets.

sourmash_index

signatures sourmash genomics metagenomics mapping kmer

Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.

Input

metasignatures

Output

meta versions signature_index

Tools

sourmash:

Compute and compare FracMinHash signatures for DNA data sets.

sourmash_sketch

hash sketch sourmash genomics metagenomics taxonomic classification taxonomic profiling kmer

Create a signature (a group of FracMinHash sketches) of a sequence using sourmash

Input

metasequence

Output

meta versions signatures

Tools

sourmash:

Compute and compare FracMinHash signatures for DNA and protein data sets.

sourmash_taxannotate

fracminhash sketch signature kmer containment sourmash genomics metagenomics taxonomic classification taxonomic profiling

Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.

Input

metagather_resultstaxonomy

Output

meta result versions

Tools

sourmash:

Compute and compare FracMinHash signatures for DNA data sets.

spaceranger_count

align count spatial spaceranger imaging

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

Input

metareadsimagecytaimagedarkimagecolorizedimagealignmentslidefilereferenceprobeset

Output

meta outs versions

Tools

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

spaceranger_mkgtf

reference mkref index spaceranger

Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.

Input

gtf

Output

gtf versions

Tools

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

spaceranger_mkref

reference mkref index spaceranger

Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.

Input

fastagtfreference_name

Output

reference versions

Tools

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

spades

genome assembly genome assembler small genome de novo assembler

Assembles a small genome (bacterial, fungal, viral)

Input

metailluminapacbionanoporeymlhmm

Output

meta scaffolds contigs transcripts gene_clusters gfa log log versions

spatyper

fasta spatype

Computational method for finding spa types.

Input

metafastarepeatsrepeat_order

Output

meta versions tsv

splitubam

long-read bam genomics

split one ubam into multiple, per line, fast

Input

metabam

bacteria fasta streptococcus

Serotype prediction of Streptococcus suis assemblies

Input

metafasta

Output

meta versions tsv

stadeniolib_scramble

sam bam cram compression

Advanced sequence file format conversions

Input

metareadsfastafaigzi

Output

meta versions reads gzi

Tools

align count genome reference

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

Input

metasolotypemeta2indexreads

Output

meta log_final log_out log_progress summary versions

stecfinder

serotype Escherichia coli fastq fasta

Serotype STEC samples from paired-end reads or assemblies

Input

metaseqs

Output

meta versions tsv

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

metaposfileinputrdatachromosome_nameKnGenmeta2collected_cramscollected_craiscramlistmeta3fastafasta_fai

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

metameta2meta3meta4meta5tumorbamtummorbainormalbamnormalbaibwa_indexfastafasta_faidbsnpdbsnp_tbiregions

Output

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

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

metameta2meta3testtest_tbitruthtruth_tbifastabed

Output

meta versions fns fps distances log report

Tools

svanalyzer:

SVanalyzer: tools for the analysis of structural variation in genomes

svdb_merge

structural variants vcf merge

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

Input

metapriorityvcfs

Output

meta versions vcf

Tools

svdb:

structural variant database software

svdb_query

structural variants query svdb

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

Input

metain_occsin_frqsvcfvcf_dbsbedpe_dbs

Output

meta versions out_occs out_frqs vcf

Tools

svdb:

structural variant database software

svtk_baftest

svtk svtk/baftest baftest baf bed structural variants

Performs tests on BAF files

Input

metabedbafbaf_indexbatch

Output

meta versions metrics

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

metavcf

Output

meta versions counts

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

metabedsamplesfasta_fai

Output

meta versions vcf tbi

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

argsmetavcffasta_fai

Output

meta versions standardized_vcf

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

metavcftbi

Output

meta versions bed

Tools

svtk:

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

svtyper_svtyper

sv structural variants genotyping

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

Input

metameta2bamvcffastafai

Output

meta versions json gt_vcf relevant_bam

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

metameta2bambam_indexvcffasta

Output

meta versions json gt_vcf

Tools

alignment MSA genomics

Aligns sequences using T_COFFEE

Input

metafastameta2treemeta3templateaccessory_informationscompress

Output

meta 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

metamsaref_msa

Output

meta versions scores

Tools

tcoffee:

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

pigz:

Parallel implementation of the gzip algorithm.

tcoffee_irmsd

alignment MSA evaluation

Computes the irmsd score for a given alignment and the structures.

Input

metamsatemplatestructures

Output

meta versions irmsd

Tools

tcoffee:

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

pigz:

Parallel implementation of the gzip algorithm.

tcoffee_seqreformat

reformatting alignment genomics

Reformats files with t-coffee

Input

metafasta

Output

meta versions formatted_file

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

metamsalib

Output

meta versions tcs scores

Tools

tcoffee:

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

nanopore sequencing quality control genomics

A post sequencing QC tool for Oxford Nanopore sequencers

Input

metaseq_summaryfastqbam

Output

meta report_data report_html plots_html plotly_js versions

transdecoder_longorf

eucaryotes gff

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

Input

metafasta

Output

meta versions pep gff3 cds dat folder

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

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

Input

metafastafold

Output

meta versions pep gff3 cds bed

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.

trimgalore

trimming adapters sequencing adapters fastq

Trim FastQ files using Trim Galore!

Input

metareads

Output

meta reads unpaired html zip log versions

trimmomatic

trimming adapter trimming quality trimming

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

Input

metareads

Output

meta 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

metareads

genomics transcript selector gene prediction evidence

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

Input

metagtfshints_fileskeep_gtfsconfig

Output

meta versions tsebra_gtf tsebra_scores

tximeta_tximport

gene kallisto pseudoalignment salmon transcript

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

Input

metaquantsmeta2tx2genemeta3coldataquant_type

Output

meta 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

metabedgraph

Output

meta versions bedgraph

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

metabedgraphsizes

Output

meta versions bigwig

Tools

ucsc:

Convert a bedGraph file to bigWig format.

ucsc_bedtobigbed

bed bigbed ucsc bedtobigbed converter

Convert file from bed to bigBed format

Input

metabedsizesautosql

Output

meta versions bigbed

Tools

ucsc:

Convert file from bed to bigBed format

ucsc_bigwigaverageoverbed

bigwig bedGraph ucsc

compute average score of bigwig over bed file

Input

metabedbigwig

Output

meta versions tab

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

metagtf

Output

meta genepred refflat versions

Tools

ucsc:

Convert GTF files to GenePred format

ucsc_liftover

bed ucsc ucsc/liftover

convert between genome builds

Input

metabed

Output

meta version lifted unlifted

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

metawigchromsizes

Output

versions bw

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

metareadsgenomepickledb

Output

meta versions bam

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

fastagtf

Output

versions pickle pickle

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

metareadsgenomegtf

Output

meta 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

metafastq

genome assembly genome assembler small genome

Assembles bacterial genomes

Input

metashortreadslongreads

Output

meta versions 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

metareads

Output

outs versions

untar

untar uncompress extract

Extract files.

Input

metaarchive

Output

meta untar versions

untarfiles

untar uncompress files

Extract files.

Input

metaarchive

Output

meta files versions

Tools

untar:

Extract tar.gz files.

unzip

unzip decompression zip archiving

Unzip ZIP archive files

Input

metaarchive

Output

meta unzipped_archive versions

unzipfiles

unzip decompression zip archiving

Unzip ZIP archive files

Input

metaarchive

Output

meta 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

metavcf

Output

meta versions bed

vardictjava

variant calling vcf bam snv sv

The Java port of the VarDict variant caller

Input

metabamsbaisbedmeta2fastameta3fasta_fai

structural_variants array_cgh vcf cytosure

Convert VCF with structural variations to CytoSure format

Input

metameta2meta3meta4sv_vcfcoverage_bedcnssnv_vcfblacklist_bed

Output

meta versions cgh

vcf2db

vcf2db vcf gemini

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

Input

metavcfped

Output

meta versions db

vcf2maf

vcf maf annotation

vcf2maf

Input

metavcfvep_cache

VCFtools VCF sort

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

Input

metavariant_filebeddiff_variant_file

Output

meta versions 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

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 turorial

Input

metabarcodesbamsorted_bamgtf

Output

meta versions loom

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

metabambairefvcf

Output

meta versions log selfsm depthsm selfrg depthrg bestsm bestrg

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

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

Input

metabambaisvd_udsvd_musvd_bedreferencesrefvcf

Output

meta mu ud bed versions log self_sm ancenstry

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

metainputtbisinsertions_fastafastafasta_fai

Output

meta versions graph

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

metagfapbgbwt

Output

meta 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

metafasta_gzpafquery_selfgzifaifasta_query_list

Output

meta paf versions

wgsim

simulate fasta reads

simulating sequence reads from a reference genome

Input

metafasta

structural-variants benchmarking vcf

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

Input

metaquery_vcftruth_vcfbed

Output

meta versions report bench_vcf bench_vcf_tbi

xengsort_index

index QC reference fasta xenograft sort k-mer

Fast lightweight accurate xenograft sorting

Input

host_fastagraft_fastaindexnobjectsmask

Output

hash info versions

Tools

xengsort:

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

xz_compress

xz compression archive

Compresses files with xz.

Input

metaraw_file

Output

meta 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

metaarchive

Output

meta file versions

Tools

unzip decompression zip archiving

Compress file lists to produce ZIP archive files

Input

metafiles

Output

meta 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