Available Modules
Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.
Calculates base frequency statistics across reference positions from BAM.
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depth_sample depth_global qs pos counts icounts versions
ANGSD: Analysis of next generation Sequencing Data
Calculated genotype likelihoods from BAM files.
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genotype_likelihood versions
ANGSD: Analysis of next generation Sequencing Data
Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.
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extracted_reads_fastq log intermediate_sam intermediate_bam intermediate_sorted_bam versions
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
Run the alignment/variant-call/consensus logic of the artic pipeline
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results bam bai bam_trimmed bai_trimmed bam_primertrimmed bai_primertrimmed fasta vcf tbi json versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
copy number profiles of tumour cells.
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allelefreqs bafs cnvs logrs metrics png purityploidy segments versions
generate VCF file from a BAM file using various calling methods
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vcf versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
Estimate the post-mortem damage patterns of DNA
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empiric exponential counts table versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
split single end read groups by length and merge paired end reads
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bam txt versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data
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fastq versions
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
removes unused references from header of sorted BAM/CRAM files.
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bam versions
This module is used to clip primer sequences from your alignments.
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bam bai versions
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).
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primary_filtered_bam contamination_bam versions
write your description here
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json versions
A command line tool to compute mapping statistics from a BAM file
Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
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fastq versions
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
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bam versions
C++ API & command-line toolkit for working with BAM data
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
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stats versions
C++ API & command-line toolkit for working with BAM data
Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
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covstats hist versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Convert BAM/GFF/GTF/GVF/PSL files to bed
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bed versions
High-performance genomic feature operations.
Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
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genomecov versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Locate and tag duplicate reads in a BAM file
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bam metrics versions
biobambam is a set of tools for early stage alignment file processing.
Merge a list of sorted bam files
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bam bam_index checksum versions
biobambam is a set of tools for early stage alignment file processing.
Parallel sorting and duplicate marking
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bam bam_index cram metrics versions
biobambam is a set of tools for early stage alignment file processing.
Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.
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bam bai versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit
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bam bai versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
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 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.
Summarize and/or filter reads based on bisulfite conversion rate
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bam versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.
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bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
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vcf versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Perform basic quality control on a BAM file generated with Biscuit
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reports versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Performs alignment of BS-Seq reads using bismark
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bam report unmapped versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Relates methylation calls back to genomic cytosine contexts.
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coverage report summary versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Removes alignments to the same position in the genome from the Bismark mapping output.
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bam report versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Extracts methylation information for individual cytosines from alignments.
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bedgraph methylation_calls coverage report mbias versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Performs alignment of BS-Seq reads using bwameth
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bam versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.
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bed bam tagAlign pairs versions
Fast alignment and preprocessing of chromatin profiles
Realign reads mapped with BWA to elongated reference genome
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bam versions
A method to improve mappings on circular genomes such as Mitochondria.
Calculates polymorphic site rates over protein coding genes
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polymut versions
Set of utilities on sequences and BAM files
Copy number variant detection from high-throughput sequencing data
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bed cnn cnr cns pdf png versions
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.
Given segmented log2 ratio estimates (.cns), derive each segmentโs absolute integer copy number
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cns versions
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.
Copy number variant detection from high-throughput sequencing data
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tsv cnn versions
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.
Generate the input coverage table for CONCOCT using a BEDFile
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tsv versions
Clustering cONtigs with COverage and ComposiTion
Merge reads that were mapped to multiple indices
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bam versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Generates a FASTA file of chromosome sizes and a fasta index file
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sizes fai gzi versions
Tools for dealing with SAM, BAM and CRAM files
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
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bam json hist log versions
DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.
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vcf vcf_tbi gvcf gvcf_tbi versions
This tool filters alignments in a BAM/CRAM file according the the specified parameters.
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bam logs versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
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bigwig bedgraph versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Computes read coverage for genomic regions (bins) across the entire genome.
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matrix versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.
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pdf matrix versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
plots cumulative reads coverages by BAM file
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pdf matrix metrics versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input.
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pdf tab versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Convert a file in FASTA format to the ELFASTA format
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elfasta log versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.
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bam logs metrics recall gvcf table activity_profile assembly_regions versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Merge split bam/sam chunks in one file
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bam versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Split bam file into manageable chunks
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bam versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Estimate repeat sizes using NGS data
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vcf json bam versions
Compute genome-wide STR profile
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locus_tsv motif_tsv str_profile versions
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Calls consensus sequences from reads with the same unique molecular tag.
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bam versions
Tools for working with genomic and high throughput sequencing data.
Collects a suite of metrics to QC duplex sequencing data.
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family_sizes duplex_family_sizes duplex_yield_metrics umi_counts duplex_qc duplex_umi_counts versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.
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
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bam cram versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
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 5โ 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.
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bam histogram versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.
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bam versions
Tools for working with genomic and high throughput sequencing data.
FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Performs local realignment around indels to correct for mapping errors
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bam versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Generates a list of locations that should be considered for local realignment prior genotyping.
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intervals versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
SNP and Indel variant caller on a per-locus basis
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vcf versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Assigns all the reads in a file to a single new read-group
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bam bai cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
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bam cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
metainputinput_indexbqsr_tableintervalsfastafaidict
meta versions bam cram
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
estimates the parameters for the DRAGstr model
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dragstr_model versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.
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hdf5 tsv versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Converts FastQ file to SAM/BAM format
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bam versions
Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Call germline SNPs and indels via local re-assembly of haplotypes
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vcf tbi bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
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cram bam crai bai metrics versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
metabamfastafaidict
meta versions output bam_index
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Merge unmapped with mapped BAM files
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Print reads in the SAM/BAM/CRAM file
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bam cram sam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Reverts SAM or BAM files to a previous state.
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Converts BAM/SAM file to FastQ format
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fastq versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Splits reads that contain Ns in their cigar string
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and unmark the marked duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
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bam bai versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
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bam cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
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output bam_index metrics versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Performs fastq alignment to a fasta reference using using gem3-mapper
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bam versions
The GEM indexer (v3).
Tool for imputation and phasing from vcf file or directly from bam files.
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phased_variants stats_coverage versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
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.
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output ped bed bed_index roc html png versions
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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vcf versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Align RNA-Seq reads to a reference with HISAT2
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bam summary fastq versions
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference
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wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
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bigwig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file
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wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
readCounter function from HMMcopy utilities, used to generate read in windows
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wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
Create a tag directory with the HOMER suite
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tagdir taginfo versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
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.
Differential gene expression analysis based on the negative binomial distribution
Empirical Analysis of Digital Gene Expression Data in R
IsoSeq - Cluster - Cluster trimmed consensus sequences
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bam pbi cluster cluster_report transcriptset hq_bam hq_pbi lq_bam lq_pbi singletons_bam singletons_pbi versions
IsoSeq - Cluster - Cluster trimmed consensus sequences
Remove polyA tail and artificial concatemers
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bam pbi consensusreadset summary report versions
IsoSeq - Scalable De Novo Isoform Discovery
IsoSeq3 - Cluster - Cluster trimmed consensus sequences
metabam
meta version bam pbi cluster cluster_report transcriptset hq_bam hq_pbi lq_bam lq_pbi singletons_bam singletons_pbi
IsoSeq3 - Cluster - Cluster trimmed consensus sequences
Remove polyA tail and artificial concatemers
metabamprimers
meta bam pbi consensusreadset summary report versions
IsoSeq3 - Scalable De Novo Isoform Discovery
Extract UMI and cell barcodes
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bam pbi versions
Iso-Seq - Scalable De Novo Isoform Discovery
Generate a consensus sequence from a BAM file using iVar
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fasta qual mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Trim primer sequences rom a BAM file with iVar
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bam log versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Call variants from a BAM file using iVar
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tsv mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)
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bed versions
Java utilities for Bioinformatics.
Plot whole genome coverage from BAM/CRAM file as SVG
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output versions
Java utilities for Bioinformatics.
Converts MAF alignments in another format.
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axt_gz bam blast_gz blasttab_gz chain_gz cram gff_gz html_gz psl_gz sam_gz tab_gz versions
LAST finds & aligns related regions of sequences.
Bayesian reconstruction of ancient DNA fragments
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bam fq_pass fq_fail unmerged_r1_fq_pass unmerged_r1_fq_fail unmerged_r2_fq_pass unmerged_r2_fq_fail log versions
Converting aligned short and long reads records from one reference to another
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bam versions
Fast and accurate coordinate conversion between assemblies
Lofreq subcommand to for insert base and indel alignment qualities
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bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Inserts indel qualities in a BAM file
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bam versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
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bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
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bam log versions
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
Map short-reads to an indexed reference genome
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bam versions
An aDNA aware short-read mapper
Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
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runtime_log fragmisincorporation_plot length_plot misincorporation lgdistribution dnacomp stats_out_mcmc_hist stats_out_mcmc_iter stats_out_mcmc_trace stats_out_mcmc_iter_summ_stat stats_out_mcmc_post_pred stats_out_mcmc_correct_prob dnacomp_genome rescaled pctot_freq pgtoa_freq fasta folder versions
Depth computation per contig step of metabat2
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depth versions
Metagenome binning of contigs
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tooshort lowdepth unbinned membership fasta versions
MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
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profile biom bt2out versions
Extracts per-base methylation metrics from alignments
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bedgraph methylkit versions
Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.
Generates methylation bias plots from alignments
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txt versions
Read position methylation bias tools from MethylDackel, a (mostly) universal extractor for methyl-seq experiments.
Taxonomic meta-omics profiling using universal marker genes
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out bam mgc log versions
Marker gene-based OTU (mOTU) profiling
A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
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mtnucratio json versions
Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.
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bam rad versions
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.
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index versions
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
AMR predictions for supported species
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csv json versions
Antibiotic resistance prediction in minutes
Compare multiple runs of long read sequencing data and alignments
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report_html lengths_violin_html log_length_violin_html n50_html number_of_reads_html overlay_histogram_html overlay_histogram_normalized_html overlay_log_histogram_html overlay_log_histogram_normalized_html total_throughput_html quals_violin_html overlay_histogram_identity_html overlay_histogram_phredscore_html percent_identity_violin_html active_pores_over_time_html cumulative_yield_plot_gigabases_html sequencing_speed_over_time_html stats_txt versions
Performs fastq alignment to a fasta reference using NextGenMap
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bam versions
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime
Determines the gender of a sample from the BAM/CRAM file.
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tsv versions
Short-read sequencing tools
Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.
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corr_matrix matched all pdf vcf versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
Calls CNVs in bam files from tumor patients
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png profile summary versions
A program to convert bam into paf.
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paf versions
A program to manipulate paf files / convert to and from paf.
Split a .pairsam file into .pairs and .sam.
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pairs bam versions
CLI tools to process mapped Hi-C data
NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).
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bam bai versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.
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bam bai cram crai bqsr_table qc_metrics duplicate_metrics versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence
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bam bai qc_metrics bqsr_table duplicate_metrics versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
Determines the depth in a BAM/CRAM file
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depth binned_depth versions
Graph realignment tools for structural variants
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.
01
bam pbi versions
PacBio BAM C++ library
Alignment with PacBio's minimap2 frontend
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bam versions
A minimap2 frontend for PacBio native data formats
converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq
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fastq versions
pbtk - PacBio BAM toolkit
Minimalistic tool which creates an index file that enables random access into PacBio BAM files
01
pbi versions
pbtk - PacBio BAM toolkit
Assigns all the reads in a file to a single new read-group
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bam bai cram versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collects hybrid-selection (HS) metrics for a SAM or BAM file.
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metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics about the insert size distribution of a paired-end library.
01
metrics histogram versions
Java tools for working with NGS data in the BAM format
Collect multiple metrics from a BAM file
0120101
metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics from a RNAseq BAM file
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metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
01201010
metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Checks that all data in the set of input files appear to come from the same individual
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crosscheck_metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.
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vcf tbi versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Converts a FASTQ file to an unaligned BAM or SAM file.
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Verify mate-pair information between mates and fix if needed
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Locate and tag duplicate reads in a BAM file
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bam bai cram metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Merges multiple BAM files into a single file
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads
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bam bai num_reads versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
changes name of sample in the vcf file
01
vcf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases
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intervals versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.
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bam bai versions
Sorts BAM/SAM files based on a variety of picard specific criteria
010
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Sorts vcf files
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vcf versions
Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
pmdtools command to filter ancient DNA molecules from others
01200
bam versions
Compute postmortem damage patterns and decontaminate ancient genomes
Run all Portcullis steps in one go
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log pass_junctions_bed pass_junctions_tab intron_gff exon_gff spliced_bam spliced_bai versions
Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes splice junctions and removes likely false positives, outputting filtered results in multiple formats for downstream analysis.
converts sam/bam/cram/pairs into genome contact map
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pretext versions
Compute summary statistics for control gene from BAM files.
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control_stats versions
A Python package for pharmacogenomics research
Call SNVs/indels from BAM files for all target genes.
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vcf tbi versions
A Python package for pharmacogenomics research
Prepare a depth of coverage file for all target genes with SV from BAM files.
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coverage versions
A Python package for pharmacogenomics research
Evaluate alignment data
010
results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Evaluate alignment data
012000
results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
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junc versions
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Quality control of riboseq bam data
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predictions all transprofile versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
Quality control of riboseq bam data
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distribution pdf offset versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
Accurate detection of short and long active ORFs using Ribo-seq data
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protocol bam_summary read_length_dist metagene_profile_5p metagene_profile_3p metagene_plots psite_offsets pos_wig neg_wig orfs versions
Python package to detect translating ORF from Ribo-seq data
Calculate expression with RSEM
010
counts_gene counts_transcript stat logs versions bam_star bam_genome bam_transcript
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Generate statistics from a bam file
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txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
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csv json bam versions
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Outputs some statistics drawn from read flags.
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stats versions
Tools for working with SAM/BAM data
find and mark duplicate reads in BAM file
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bam bai versions
process your BAM data faster!
This module combines samtools and samblaster in order to use samblaster capability to filter or tag SAM files, with the advantage of maintaining both input and output in BAM format. Samblaster input must contain a sequence header: for this reason it has been piped with the "samtools view -h" command. Additional desired arguments for samtools can be passed using: options.args2 for the input bam file options.args3 for the output bam file
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bam versions
Clips read alignments where they match BED file defined regions
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bam stats rejects_bam versions
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.
The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format
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reads versions
Tools for dealing with SAM, BAM and CRAM files
calculates MD and NM tags
0101
bam versions
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.
Concatenate BAM or CRAM file
01
bam cram versions
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.
shuffles and groups reads together by their names
0101
bam cram sam versions
Tools for dealing with SAM, BAM and CRAM files
The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format
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fastq fastq_interleaved fastq_other fastq_singleton versions
Tools for dealing with SAM, BAM and CRAM files
Produces a consensus FASTA/FASTQ/PILEUP
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fasta fastq pileup versions
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.
convert and then index CRAM -> BAM or BAM -> CRAM file
0120101
bam cram bai crai versions
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.
produces a histogram or table of coverage per chromosome
0120101
coverage versions
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.
List CRAM Content-ID and Data-Series sizes
01
size versions
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.
Computes the depth at each position or region.
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tsv versions
Tools for dealing with SAM, BAM and CRAM files; samtools depth โ computes the read depth at each position or region
Create a sequence dictionary file from a FASTA file
01
dict versions
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.
Index FASTA file, and optionally generate a file of chromosome sizes
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fa fai sizes gzi versions
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.
Converts a SAM/BAM/CRAM file to FASTA
010
fasta interleaved singleton other versions
Tools for dealing with SAM, BAM and CRAM files
Converts a SAM/BAM/CRAM file to FASTQ
010
fastq interleaved singleton other versions
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 is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
01
bam cram sam versions
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.
Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
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flagstat versions
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.
filter/convert SAM/BAM/CRAM file
01
readgroup versions
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.
Reports alignment summary statistics for a BAM/CRAM/SAM file
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idxstats versions
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.
converts FASTQ files to unmapped SAM/BAM/CRAM
01
sam bam cram versions
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.
Index SAM/BAM/CRAM file
01
bai csi crai versions
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.
mark duplicate alignments in a coordinate sorted file
0101
bam cram sam versions
Tools for dealing with SAM, BAM and CRAM files
Merge BAM or CRAM file
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bam cram csi crai versions
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.
BAM
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mpileup versions
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.
Replace the header in the bam file with the header generated by the command. This command is much faster than replacing the header with a BAMโSAMโBAM conversion.
01
bam versions
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.
Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file
0101
bam cram csi crai metrics versions
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 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 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 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 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.
Sort SAM/BAM/CRAM file
0101
bam cram crai csi versions
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.
Produces comprehensive statistics from SAM/BAM/CRAM file
01201
stats versions
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.
filter/convert SAM/BAM/CRAM file
0120100
bam cram sam bai csi crai unselected unselected_index versions
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.
The cluster_identifier tool of Scramble identifies soft clipped clusters
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clusters versions
Soft Clipped Read Alignment Mapper
Performs fastq alignment to a fasta reference using Sentieon's BWA MEM
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bam_and_bai versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Collects multiple quality metrics from a bam file
01201010
mq_metrics qd_metrics gc_summary gc_metrics aln_metrics is_metrics mq_plot qd_plot is_plot gc_plot versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.
0120101
cram crai bam bai score metrics metrics_multiqc_tsv versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.
0120101
output index output_index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Collects whole genome quality metrics from a bam file
012010101
wgs_metrics versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Sequence quality metrics for FASTQ and uBAM files.
01
json html versions
PileupCaller is a tool to create genotype calls from bam files using read-sampling methods
0100
eigenstrat plink freqsum versions
Tools for population genetics on sequencing data
Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
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seqz versions
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.
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.
01
wig versions
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.
tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2ฮ7โ8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
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smncopynumber run_metrics versions
Rapid haploid variant calling
010
tab csv html vcf bed gff bam bai log aligned_fa consensus_fa consensus_subs_fa raw_vcf filt_vcf vcf_gz vcf_csi txt versions
Rapid bacterial SNP calling and core genome alignments
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
01012
tsv html versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
012010101
extract versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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html pairs_tsv samples_tsv versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
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gene_results fullgene_results mlst_results pileup sorted_bam versions
Short Read Sequence Typing for Bacterial Pathogens
Advanced sequence file format conversions
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cram gzi versions
Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
Align reads to a reference genome using STAR
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log_final log_out log_progress versions bam bam_sorted bam_sorted_aligned bam_transcript bam_unsorted fastq tab spl_junc_tab read_per_gene_tab junction sam wig bedgraph
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
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.
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input rdata plots vcf bgen versions
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data
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json gt_vcf bam versions
Compute genotype of structural variants based on breakpoint depth
A tool to detect resistance and lineages of M. tuberculosis genomes
01
bam csv json txt vcf versions
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
Computes the coverage of different regions from the bam file.
0101
cov wig versions
TIDDIT - structural variant calling.
Tandem repeat genotyping from PacBio HiFi data
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vcf bam versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
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bam fastq log versions
Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
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bam log tsv_edit_distance tsv_per_umi tsv_umi_per_position versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Group reads based on their UMI and mapping coordinates
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log bam tsv versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Make the output from umi_tools dedup or group compatible with RSEM
012
bam log versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
The Java port of the VarDict variant caller
01230101
vcf versions
Filtering, downsampling and profiling alignments in BAM/CRAM formats
01
bam versions
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.bamSee module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:
withName: SAMTOOLS_SORT {
ext.prefix = { "cellsorted_${bam.baseName}" }
ext.args = '-t CB -O BAM'
}Optional mask must be passed with ext.args and option --mask
This is why I need to stage in the work dir 2 bam files (cellsorted and original).
See also velocyto tutorial
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loom versions
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log selfsm depthsm selfrg depthrg bestsm bestrg versions
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.
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log ud bed mu self_sm ancestry versions
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.
01
aln biom mothur otu bam out blast uc centroids clusters profile msa versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
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vcf tbi graph versions
Convert and filter aligned reads to .npz
0120101
npz versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
Align reads to a reference genome using YARA
0101
bam bai versions
Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
Click here to trigger an update.