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.
Trim sequencing adapters and collapse overlapping reads
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singles_truncated discarded paired_truncated collapsed collapsed_truncated paired_interleaved settings versions
The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
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passed_gff failed_gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
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.
Simulation tool to generate synthetic Illumina next-generation sequencing reads
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fastq aln sam versions
ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.
Aggregates fastq files with demultiplexed reads
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fastq versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
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
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
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
Adapter and quality trimming of sequencing reads
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reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Merging overlapping paired reads into a single read.
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merged unmerged ihist versions log
BBMap is a short read aligner, as well as various other bioinformatic tools.
BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.
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fastq log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates
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reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Filter out sequences by sequence header name(s)
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reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Re-pairs reads that became disordered or had some mates eliminated.
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repaired singleton versions log
Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.
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.
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
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.
Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.
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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.
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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.
Collects bismark alignment reports
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report versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.
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summary 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 indexing of c2t converted reference genome
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index versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
Concatenates fastq files
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reads versions
The cat utility reads files sequentially, writing them to the standard output.
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
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txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
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orf2lca bin2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
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orf2lca contig2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
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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)
Summarises results from CAT/BAT/RAT classification steps
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txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
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outs versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.
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fastq undetermined_fastq reports stats interop versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
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gtf versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
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reference versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.
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config outs versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.
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versions fastq
Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command.
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gtf versions
Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command.
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versions fastq
Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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.
CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.
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root tab versions
Tool for calling copy number variations.
Calculates peak-to-through ratio (PTR) from metagenomic sequence data
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ptr versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Computes the coverage map along the reference genome
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coverage versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Indexes a directory of fasta files for use with CoPTR
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index_dir versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
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.
Map reads to contigs and estimate coverage
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coverage versions
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
Perform adapter/quality trimming on sequencing reads
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reads log versions
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
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 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
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
Assemble bacterial isolate genomes from Nanopore reads
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contigs log raw_contigs gfa txt versions
Export assembly segment sequences in GFA 1.0 format to FASTA format
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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
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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
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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
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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
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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.
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
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vcf versions
Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
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vcf tbi versions
A taxonomic profiler for metagenomic 16S data optimized for error prone long reads.
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report assignment_report samfile unclassified_fa versions
Emu is a relative abundance estimator for 16s genomic data.
Run falco on sequenced reads
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html txt versions
falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Perform adapter and quality trimming on sequencing reads with reporting
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reads stats debug statspdf reads_fail reads_unpaired log versions
A program that counts sequence occurrences in FASTQ files.
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count_matrix stats distribution_plot reads_plot reads_plot_percentage versions
2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.
Perform adapter/quality trimming on sequencing reads
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reads json html log reads_fail reads_merged versions
Align reads to multiple reference genomes using fastq-screen
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txt png html fastq versions
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)
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fasta versions
A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
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.
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
Filtlong filters long reads based on quality measures or short read data.
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reads log versions
Perform merging of mate paired-end sequencing reads
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merged notcombined histogram versions
De novo assembler for single molecule sequencing reads
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fasta gfa gv txt log json versions
fq generate is a FASTQ file pair generator. It creates two reads, formatting names as described by Illumina. While generate creates "valid" FASTQ reads, the content of the files are completely random. The sequences do not align to any genome. This requires a seed (--seed) to be supplied in ext.args.
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fastq versions
fq is a library to generate and validate FASTQ file pairs.
Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.
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lineages summarized versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
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.
Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
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contamination segmentation 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.
Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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split_read_evidence split_read_evidence_index paired_end_evidence paired_end_evidence_index site_depths site_depths_index versions
Genome Analysis Toolkit (GATK4)
Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
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table 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.
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.
WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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printed_evidence printed_evidence_index 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.
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.
Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
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linear_plot_png transformed_linear_plot_png log_plot_png transformed_log_plot_png model summary lookup_table fitted_histogram_png versions
Assembles organelle genomes from genomic data
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fasta etc versions
Get organelle genomes from genome skimming data
Collapse redundant transcript models in Iso-Seq data.
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bed bed_trans_reads local_density_error polya read strand_check trans_report versions varcov variants
Collapse similar gene model
Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)
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fasta report tails versions
Gene-Switch Transcriptome Annotation by Modular Algorithms
Whole-genome assembly using PacBio HiFi reads
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raw_unitigs bin_files processed_unitigs primary_contigs alternate_contigs hap1_contigs hap2_contigs corrected_reads read_overlaps log versions
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.
Builds HISAT2 index for reference genome
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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
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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.
Pre-compute the graph index structure.
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graph versions
HLA typing from short and long reads
Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.
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results extraction extraction_mapped extraction_unmpapped hla fastq reads_per_level remapped versions
HLA typing from short and long reads
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
count how many reads map to each feature
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txt versions
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.
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log dedup annotated stats versions
Remove polyA tail and artificial concatemers
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bam pbi consensusreadset summary report versions
IsoSeq - Scalable De Novo Isoform Discovery
Remove polyA tail and artificial concatemers
metabamprimers
meta bam pbi consensusreadset summary report versions
IsoSeq3 - Scalable De Novo Isoform Discovery
Create kallisto index
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index versions
Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Computes equivalence classes for reads and quantifies abundances
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results json_info log versions
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.
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reads versions
khmer k-mer counting library
Removes low abundance k-mers from FASTA/FASTQ files
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trimmed versions
khmer k-mer counting library
Classifies metagenomic sequence data
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classified_reads_fastq unclassified_reads_fastq classified_reads_assignment report versions
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
Extract reads classified at any user-specified taxonomy IDs.
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extracted_kraken2_reads versions
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
Classifies metagenomic sequence data using unique k-mer counts
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classified_reads unclassified_reads classified_assignment report versions
Metagenomics classifier with unique k-mer counting for more specific results
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
mageck count for functional genomics, reads are usually mapped to a specific sgRNA
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count norm versions
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.
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vcf tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi somatic_sv_vcf somatic_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi tumor_sv_vcf tumor_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
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
Analyses a DAA file and exports information in text format
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txt_gz megan versions
A tool for studying the taxonomic content of a set of DNA reads
Analyses an RMA file and exports information in text format
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txt megan_summary versions
A tool for studying the taxonomic content of a set of DNA reads
Performs taxonomic profiling of long metagenomic reads against the melon database
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tsv_output json_output log versions
Compare k-mer frequency in reads and assembly to devise the metrics K and QV
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hist log_stderr versions
Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of Merqury) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.
Strain-level metagenomic assignment
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wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions
Maps long reads to a metamaps database
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classification_res meta_file meta_unmappedreadsLengths para_file versions
Metagenome assembler for long-read sequences (HiFi and ONT).
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contigs log versions
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.
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outputs versions
miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.
miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.
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outputs versions
miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs.
It includes three main scripts: miRDeep2.pl, mapper.pl, and quantifier.pl for comprehensive miRNA detection and quantification.
A python workflow that assembles mitogenomes from Pacbio HiFi reads
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fasta stats gb gff all_potential_contigs contigs_annotations contigs_circularization contigs_filtering coverage_mapping coverage_plot final_mitogenome_annotation final_mitogenome_choice final_mitogenome_coverage potential_contigs reads_mapping_and_assembly shared_genes versions
A python workflow that assembles mitogenomes from Pacbio HiFi reads
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
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
Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"
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insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions
nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.
Run NanoPlot on nanopore-sequenced reads
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html png txt log versions
Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.
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stats reads versions
Merging paired-end reads and removing sequencing adapters.
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merged_reads unstitched_read1 unstitched_read2 versions
Determines the gender of a sample from the BAM/CRAM file.
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tsv versions
Short-read sequencing tools
write your description here
metareadsformatmode
meta versions npa npc npl npo
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
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.
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.
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.
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.
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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xml txt versions
Polishing genome assemblies with short reads.
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fasta versions debug
Polishing genome assemblies with short reads.
Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.
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cel plp var umi versions
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools
Extension of Porechop whose purpose is to process adapter sequences in ONT reads.
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reads log versions
Adapter removal and demultiplexing of Oxford Nanopore reads
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reads log versions
Adapter removal and demultiplexing of Oxford Nanopore reads
Filter reads by quality score.
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reads logs versions log_tab
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
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good_reads single_reads bad_reads log versions
frame-shift correction for long read (meta)genomics - fix frameshifts in reads
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out_fa versions
frame-shift correction for long read (meta)genomics
frame-shift correction for long read (meta)genomics - maps proteins to reads
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tsv versions
frame-shift correction for long read (meta)genomics
reads a maxQuant proteinGroups file with Proteus
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dendro_plot mean_var_plot raw_dist_plot norm_dist_plot raw_rdata norm_rdata raw_tab norm_tab session_info versions
R package for analysing proteomics data
Randomly subsample sequencing reads to a specified coverage
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reads versions
De novo genome assembler for long uncorrected reads.
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fasta gfa versions
Infer strandedness from sequencing reads
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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.
Calculate how mapped reads are distributed over genomic features
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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.
Calculate TIN (transcript integrity number) from RNA-seq reads
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txt xls versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
SALSA, A tool to scaffold long read assemblies with HiC
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fasta agp agp_original_coordinates versions
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
find and mark duplicate reads in BAM file
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bam bai versions
process your BAM data faster!
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
shuffles and groups reads together by their names
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bam cram sam versions
Tools for dealing with SAM, BAM and CRAM files
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.
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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.
Call peaks using SEACR on sequenced reads in bedgraph format
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bed versions
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).
Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm
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vcf tbi 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.
Create BWA index for reference genome
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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.
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.
Accelerated implementation of the Picard CollectVariantCallingMetrics tool.
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metrics summary 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.
Accelerated implementation of the GATK DepthOfCoverage tool.
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per_locus sample_summary statistics coverage_counts coverage_proportions interval_summary 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
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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.
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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.
modifies the input VCF file by adding the MLrejected FILTER to the variants
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vcf 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.
DNAscope algorithm performs an improved version of Haplotype variant calling.
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vcf vcf_tbi gvcf gvcf_tbi 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.
Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.
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vcf_gz vcf_gz_tbi 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 Sentieon's haplotyper for germline variant calling.
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vcf vcf_tbi gvcf gvcf_tbi 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
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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.
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.
Filters the raw output of sentieon/tnhaplotyper2.
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vcf vcf_tbi stats 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.
Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.
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orientation_data contamination_data contamination_segments stats vcf 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.
TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.
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vcf 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.
Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm
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recal idx tranches plots 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.
match up paired-end reads from two fastq files
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reads unpaired_reads versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Split single or paired-end fastq.gz files
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reads versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Salmonella serotype prediction from reads and assemblies
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log tsv txt versions
Generates a BED file containing genomic locations of lengths of N.
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bed versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
Interleave pair-end reads from FastQ files
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reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
Subsample reads from FASTQ files
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reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
Trim low quality bases from FastQ files
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reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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tsv txt versions
SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
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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
The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.
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assembly gfa results versions
Determine Shigella serotype from Illumina or Oxford Nanopore reads
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tsv hits versions
Determine Shigella serotype from assemblies or Illumina paired-end reads
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tsv versions
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.
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vcf versions
structural variant calling and genotyping with existing tools, but, smoothly
Local sequence alignment tool for filtering, mapping and clustering.
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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.
Fast, efficient, lossless compression of FASTQ files.
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spring versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
Fast, efficient, lossless decompression of FASTQ files.
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fastq versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
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reads versions
SRA Toolkit and SDK from NCBI
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.
Serotype STEC samples from paired-end reads or assemblies
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tsv versions
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
Tandem repeat genotyper for long reads
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vcf tbi versions
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
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vcf vcf_tbi genome_vcf genome_vcf_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
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vcf_indels vcf_indels_tbi vcf_snvs vcf_snvs_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Count reads that map to genomic features
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counts summary versions
featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
Sketching/indexing sequencing reads
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sketch_fastq_genome versions
Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
Trim FastQ files using Trim Galore!
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reads log unpaired html zip versions
Performs quality and adapter trimming on paired end and single end reads
01
trimmed_reads unpaired_reads trim_log out_log summary versions
Assembles a de novo transcriptome from RNAseq reads
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transcript_fasta log versions
Subsample a long-read sequencing fastq file for multiple assemblies
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subreads versions
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes
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
Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
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reads log 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
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.
Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.
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rnafold_txt rnafold_ps versions
Calculate minimum free energy secondary structures and partition function of RNAs
The program reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. If not specified differently using commandline arguments, input is accepted from stdin or read from an input file, and output printed to stdout. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.
A tool of the wipertools suite that fixes or wipes out uncompliant reads from FASTQ files
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wiped_fastq report versions
A tool of the wipertools suite that that fixes or wipes out uncompliant reads from FASTQ files.
Convert and filter aligned reads to .npz
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npz versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
Align reads to a reference genome using YARA
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bam bai versions
Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
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