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.
Post-processing script of the MaltExtract component of the HOPS package
000
json summary_pdf tsv candidate_pdfs versions
Run the alignment/variant-call/consensus logic of the artic pipeline
01012012
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
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
0100
tif versions
Generate tables of feature metadata from GTF files
0101
feature_annotation filtered_cdna versions
Scripts for manipulating gene annotation
This module is used to clip primer sequences from your alignments.
0123
bam bai versions
Merging overlapping paired reads into a single read.
010
merged unmerged ihist versions log
BBMap is a short read aligner, as well as various other bioinformatic tools.
Locate and tag duplicate reads in a BAM file
01
bam metrics versions
biobambam is a set of tools for early stage alignment file processing.
Merge a list of sorted bam files
01
bam bam_index checksum versions
biobambam is a set of tools for early stage alignment file processing.
Parallel sorting and duplicate marking
0101
bam bam_index cram metrics versions
biobambam is a set of tools for early stage alignment file processing.
A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit
010101
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.
Performs alignment of BS-Seq reads using bismark
010101
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.
Removes alignments to the same position in the genome from the Bismark mapping output.
01
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.
Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.
01
index 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.
0101
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.
Collects bismark alignment reports
01234
report versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database
01010
xml tsv csv versions
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
Construct species phylogenies using BUSCO proteins
01
gene_trees supermatrix versions
Construct species phylogenies using BUSCO proteins
Performs alignment of BS-Seq reads using bwameth
010101
bam versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
Performs indexing of c2t converted reference genome
01
index versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
0101010101001010101010101
rat_log complete_abundance contig_abundance read2classification alignment_diamond contig2classification cat_log orf2lca faa gff unmapped_diamond unmapped_fasta unmapped2classification versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Cluster protein sequences using sequence similarity
01
fasta clusters versions
Clusters and compares protein or nucleotide sequences
Cluster nucleotide sequences using sequence similarity
01
fasta clusters versions
Clusters and compares protein or nucleotide sequences
Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.
01234
base cell sample allele_depth depth_coverage depth_other versions
Efficient genotyping bi-allelic SNPs on single cells
Classifies metagenomic sequence data
01000
report results sam fastq_mapped fastq_unmapped versions
Centrifuge is a classifier for metagenomic sequences.
Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.
0101010000
bed bam tagAlign pairs versions
Fast alignment and preprocessing of chromatin profiles
Indexes a fasta reference genome ready for chromatin profiling.
01
index versions
Fast alignment and preprocessing of chromatin profiles
Predict recomination events in bacterial genomes
012
emsim em status newick fasta pos_ref versions
Align sequences using Clustal Omega
010100000
alignment versions
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
Parallel implementation of the gzip algorithm.
Renders a guidetree in clustalo
01
tree versions
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.
0101000
tx2gene versions
"Custom module to create a transcript to gene mapping from a GTF and check it against transcript quantifications"
This tool filters alignments in a BAM/CRAM file according the the specified parameters.
012
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.
01200
bigwig bedgraph versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Transforms the input alignments to a format suitable for the deep neural network variant caller
012301010101
examples gvcf small_model_calls versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
calculate clusters of highly similar sequences
01
tsv versions
Accelerated BLAST compatible local sequence aligner
Export assembly segment sequences in GFA 1.0 format to FASTA format
01
fasta versions
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.
Filter features in gzipped BED format
01
bed versions
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.
Filter features in gzipped GFF3 format
01
gff3 versions
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.
Split features in gzipped BED format
01
bed versions
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.
Split features in gzipped GFF3 format
01
gff3 versions
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.
Fast genome-wide functional annotation through orthology assignment.
010001
annotations orthologs hits versions
cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.
01
consensus versions
The European Molecular Biology Open Software Suite
A taxonomic profiler for metagenomic 16S data optimized for error prone long reads.
010
report assignment_report samfile unclassified_fa versions
Emu is a relative abundance estimator for 16s genomic data.
splits an alignment into reference and query parts
012
query reference versions
Massively parallel phylogenetic placement of genetic sequences
Aligns sequences using FAMSA
01010
alignment versions
Algorithm for large-scale multiple sequence alignments
Renders a guidetree in famsa
01
tree versions
Algorithm for large-scale multiple sequence alignments
FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM
01010101
bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Creates a database for Foldmason.
01
db versions
Multiple Protein Structure Alignment at Scale with FoldMason
Aligns protein structures using foldmason
01010
msa_3di msa_aa versions
Multiple Protein Structure Alignment at Scale with FoldMason
Renders a visualization report using foldmason
01010101
html versions
Multiple Protein Structure Alignment at Scale with FoldMason
Demultiplex fastq files
0123
sample_fastq metrics most_frequent_unmatched versions
Performs local realignment around indels to correct for mapping errors
012301010101
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.
01201010101
intervals versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
01234567010101
vcf tbi stats 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.
Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts
01
artifactprior 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.
Merge unmapped with mapped BAM files
0120101
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.
Performs fastq alignment to a fasta reference using using gem3-mapper
01010
bam versions
The GEM indexer (v3).
create index file for genmap
01
index versions
Ultra-fast computation of genome mappability.
create mappability files for a genome
0101
wig bedgraph txt csv versions
Ultra-fast computation of genome mappability.
for annotating regions, frequencies, cadd scores
01
vcf versions
Annotate genetic inheritance models in variant files
Score compounds
01
vcf versions
Annotate genetic inheritance models in variant files
annotate models of inheritance
0120
vcf versions
Annotate genetic inheritance models in variant files
Score the variants of a vcf based on their annotation
0120
vcf versions
Annotate genetic inheritance models in variant files
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
0
fasta gff vcf stats phylip embl_predicted embl_branch tree tree_labelled versions
Reformat a Multiple Sequence Alignment (MSA) file
0100
msa versions
HH-suite3 for fast remote homology detection and deep protein annotation
Align RNA-Seq reads to a reference with HISAT2
010101
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.
Builds HISAT2 index for reference genome
010101
index 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.
Extracts splicing sites from a gtf files
01
txt 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.
Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.
0123
results extraction extraction_mapped extraction_unmpapped hla fastq reads_per_level remapped versions
HLA typing from short and long reads
Mask multiple sequence alignments
012345670
maskedaln fmask_rf fmask_all gmask_rf gmask_all pmask_rf pmask_all versions
Biosequence analysis using profile hidden Markov models
hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
010
sto versions
Biosequence analysis using profile hidden Markov models
create an hmm profile from a multiple sequence alignment
010
hmm hmmbuildout versions
Biosequence analysis using profile hidden Markov models
R script that scores output from multiple runs of hmmer/hmmsearch
01
hmmrank versions
Biosequence analysis using profile hidden Markov models
A Language and Environment for Statistical Computing
Tidyverse: R packages for data science
search profile(s) against a sequence database
012345
output alignments target_summary domain_summary versions
Biosequence analysis using profile hidden Markov models
Create a tag directory with the HOMER suite
010
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
Search covariance models against a sequence database
01200
output alignments target_summary versions
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.
012000000000000
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
Aligns sequences using kalign
010
alignment versions
Kalign is a fast and accurate multiple sequence alignment algorithm.
Computes equivalence classes for reads and quantifies abundances
01010000
results json_info log versions
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Classifies metagenomic sequence data
01000
classified_reads_fastq unclassified_reads_fastq classified_reads_assignment report versions
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
Classifies metagenomic sequence data using unique k-mer counts
012000000
classified_reads unclassified_reads classified_assignment report versions
Metagenomics classifier with unique k-mer counting for more specific results
Prepare sequences for subsequent alignment with lastal.
01
index versions
LAST finds & aligns related regions of sequences.
Converts MAF alignments in another format.
012010101
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.
Reorder alignments in a MAF file
01
maf versions
LAST finds & aligns related regions of sequences.
Post-alignment masking
01
maf versions
LAST finds & aligns related regions of sequences.
Find suitable score parameters for sequence alignment
010
param_file multiqc versions
LAST finds & aligns related regions of sequences.
Align sequences using learnMSA
01
alignment versions
learnMSA: Learning and Aligning large Protein Families
Bayesian reconstruction of ancient DNA fragments
01
bam fq_pass fq_fail unmerged_r1_fq_pass unmerged_r1_fq_fail unmerged_r2_fq_pass unmerged_r2_fq_fail log versions
Typing of clinical and environmental isolates of Legionella pneumophila
01
tsv versions
Lofreq subcommand to for insert base and indel alignment qualities
010
bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments
0120
vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0123450101
vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0101
bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0120
peak xls versions gapped bed bdg
Model Based Analysis for ChIP-Seq data
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0120
peak xls versions gapped bed bdg
Model Based Analysis for ChIP-Seq data
Multiple sequence alignment using MAFFT
0101010101010
fas versions
Parallel implementation of the gzip algorithm.
Multiple sequence alignment using MAFFT
0101010101010
fas versions
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
Parallel implementation of the gzip algorithm.
Guide tree rendering using MAFFT
01
tree versions
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
Multiple Sequence Alignment using Graph Clustering
01010
alignment versions
Multiple Sequence Alignment using Graph Clustering
Multiple Sequence Alignment using Graph Clustering
01
tree versions
Multiple Sequence Alignment using Graph Clustering
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.
0000
index versions log
A tool for mapping metagenomic data
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.
010
rma6 alignments log versions
A tool for mapping metagenomic data
Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening
0100
results versions
Map short-reads to an indexed reference genome
01010000000
bam versions
An aDNA aware short-read mapper
Screens query sequences against large sequence databases
0101
screen versions
Fast sequence distance estimator that uses MinHash
Strain-level metagenomic assignment
012340
wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions
Maps long reads to a metamaps database
010
classification_res meta_file meta_unmappedreadsLengths para_file versions
Extracts per-base methylation metrics from alignments
01200
bedgraph methylkit versions
Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.
Generates methylation bias plots from alignments
01200
txt versions
Read position methylation bias tools from MethylDackel, a (mostly) universal extractor for methyl-seq experiments.
Provides fasta index required by minimap2 alignment.
01
index versions
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
Provides fasta index required by miniprot alignment.
01
index versions
A versatile pairwise aligner for genomic and protein sequences.
Aligns protein structures using mTM-align
010
alignment structure versions
Algorithm for structural multiple sequence alignments
Parallel implementation of the gzip algorithm.
SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA
010101010000001
full_alignment info_txt snp_alignment snp_genome_alignment snpstatistics snptable snptable_snpeff snptable_uncertainty structure_genotypes structure_genotypes_nomissing json versions
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
01
aligned_fasta phyi phys clustalw html msf tree log versions
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.
010
alignment versions
Muscle v5 is a major re-write of MUSCLE based on new algorithms.
Parallel implementation of the gzip algorithm.
Compare multiple runs of long read sequencing data and alignments
01
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
Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
00
dataset versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
010
csv csv_errors csv_insertions tsv json json_auspice ndjson fasta_aligned fasta_translation nwk versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Performs fastq alignment to a fasta reference using NextGenMap
010
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
NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
012
delta coords versions
Create a decoy peptide database from a standard FASTA database.
01
decoy_fasta versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Filters peptide/protein identification results by different criteria.
01
mzml featurexml consensusxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Filters peptide/protein identification results by different criteria.
012
filtered versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Calculates a distribution of the mass error from given mass spectra and IDs.
012
frag_err prec_err versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Merges several idXML files into one idXML file.
01
idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Split a merged identification file into their originating identification files
01
idxmls versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Switches between different scores of peptide or protein hits in identification data
01
idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
A tool for peak detection in high-resolution profile data (Orbitrap or FTICR)
01
mzml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Refreshes the protein references for all peptide hits.
012
indexed_idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Annotates MS/MS spectra using Comet.
012
idxml pin versions
A fast and scalable tool for bacterial pangenome analysis
01
results aln versions
panaroo - an updated pipeline for pangenome investigation
Phylogenetic Assignment of Named Global Outbreak LINeages
010
report versions
Phylogenetic Assignment of Named Global Outbreak LINeages
Phylogenetic Assignment of Named Global Outbreak LINeages
0
db versions
Phylogenetic Assignment of Named Global Outbreak LINeages
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.
01010101010
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
0101010
bam bai qc_metrics bqsr_table duplicate_metrics versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
Determines the depth in a BAM/CRAM file
0120101
depth binned_depth versions
Graph realignment tools for structural variants
Genotype structural variants using paragraph and grmpy
0123450101
vcf json versions
Graph realignment tools for structural variants
Convert a VCF file to a JSON graph
0101
graph versions
Graph realignment tools for structural variants
Alignment with PacBio's minimap2 frontend
0101
bam versions
A minimap2 frontend for PacBio native data formats
Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
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.
Collects hybrid-selection (HS) metrics for a SAM or BAM file.
01234010101
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
01000
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
01234501
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.
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.
This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.
0101
bam bai versions
Run all Portcullis steps in one go
010101
log bed tab 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.
Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'.
0120
txt png loess_qc_txt loess_txt versions
Copy number calling and SNV classification using targeted short read sequencing
Split fasta file by 'N's to aid in self alignment for duplicate purging
01
split_fasta versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
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.
Evaluate alignment data
0101
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.
Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.
0
stockholm_alignment phylogeny versions
Calculate pan-genome from annotated bacterial assemblies in GFF3 format
01
results aln versions
Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
0120
csv json bam versions
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Clips read alignments where they match BED file defined regions
01000
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.
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.
Produces a consensus FASTA/FASTQ/PILEUP
01
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.
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
01010
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 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
012
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
012
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
010101
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
0120
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 Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier
0100
meis_tab dels_tab vcf versions
Soft Clipped Read Alignment Mapper
The cluster_identifier tool of Scramble identifies soft clipped clusters
0120
clusters versions
Soft Clipped Read Alignment Mapper
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
0100
alignment trans_alignments multi_bed single_bed versions
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Performs fastq alignment to a fasta reference using Sentieon's BWA MEM
01010101
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.
Generate recalibration table and optionally perform base quality recalibration
01201010101010
table table_post recal_alignment csv pdf 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.
Induce a variation graph in GFA format from alignments in PAF format
012
gfa versions
seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
01234501
log read_qual breakpoints_double read_alignments read_ids collapsed_dup loh all_vcf all_breakpoints_clusters_list all_breakpoints_clusters all_plots somatic_vcf somatic_breakpoints_clusters_list somatic_breakpoints_clusters somatic_plots versions
Demultiplex bgzip'd fastq files
012
sample_fastq metrics most_frequent_unmatched per_project_metrics per_sample_metrics sample_barcode_hop_metrics versions
Simple ANI calculation between reference and query genomes.
0101
dist versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Memory-efficient ANI database queries with skani.
0101
search versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Storing skani sketches/indices on disk.
01
sketch_dir sketch markers versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
All-to-all ANI computation.
01
triangle versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.
01230101
vcf versions
structural variant calling and genotyping with existing tools, but, smoothly
Create a SNAP index for reference genome
01234
index versions
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
Core-SNP alignment from Snippy outputs
0120
aln full_aln tab vcf txt versions
Rapid bacterial SNP calling and core genome alignments
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
Local sequence alignment tool for filtering, mapping and clustering.
010101
reads log index versions
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.
Compare many FracMinHash signatures generated by sourmash sketch.
01000
matrix labels csv versions
Compute and compare FracMinHash signatures for DNA and protein data sets.
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.
0100000
result unassigned matches prefetch prefetchcsv versions
Compute and compare FracMinHash signatures for DNA data sets.
Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.
010
result versions
Compute and compare FracMinHash signatures for DNA data sets.
Aligns sequences using T_COFFEE
01010120
alignment lib versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Compares 2 alternative MSAs to evaluate them.
012
scores versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Computes a consensus alignment using T_COFFEE
01010
alignment eval versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats the header of PDB files with t-coffee
01
formatted_pdb versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Computes the irmsd score for a given alignment and the structures.
01012
irmsd versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package
01010120
alignment versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats files with t-coffee
01
formatted_file versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
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.
0101
tcs scores versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.
01
pep gff3 cds dat folder versions
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 identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf
010
pep gff3 cds bed versions
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.
Import transcript-level abundances and estimated counts for gene-level analysis packages
01010
tpm_gene counts_gene counts_gene_length_scaled counts_gene_scaled lengths_gene tpm_transcript counts_transcript lengths_transcript versions
Filtering, downsampling and profiling alignments in BAM/CRAM formats
01
bam versions
In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.
010101
alignment_properties_json versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Constructs a graph from a reference and variant calls or a multiple sequence alignment file
01230101
graph versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
Deconstruct snarls present in a variation graph in GFA format to variants in VCF format
0100
vcf versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
write your description here
01
xg vg_index versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
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)
Performs quality filtering and / or conversion of a FASTQ file to FASTA format.
01
fasta log 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)
Taxonomic classification using the sintax algorithm.
010
tsv 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)
Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).
010
fasta 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)
Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
010000
aln biom lca mothur otu sam tsv txt uc 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)
a pangenome-scale aligner
0123400
paf versions
Click here to trigger an update.