modules.mdx

title	Supported Tools
description	Tools supported by MultiQC
displayed_sidebar	multiqcSidebar

MultiQC currently has modules to support 181 bioinformatics tools, listed below.

Click the tool name to go to the MultiQC documentation for that tool.

:::tip[Missing something?] If you would like another tool to to be supported, please open an issue. :::

import MultiqcModules from "@site/src/components/MultiqcModules";

<MultiqcModules modules={[ { id: "modules/adapterremoval", data: { name: "Adapter Removal", summary: "Removes adapter sequences, trims low quality bases from 3' ends, or merges overlapping pairs into consensus.", }, }, { id: "modules/afterqc", data: { name: "AfterQC", summary: "Automatic filtering, trimming, error removing, and quality control for FastQ data.", }, }, { id: "modules/anglerfish", data: { name: "Anglerfish", summary: "Quality controls Illumina libraries sequenced on Oxford Nanopore flowcells.", }, }, { id: "modules/ataqv", data: { name: "ATAQV", summary: "Toolkit for quality control and visualization of ATAC-seq data." }, }, { id: "modules/bakta", data: { name: "Bakta", summary: "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids." }, }, { id: "modules/bamdst", data: { name: "Bamdst", summary: "Lightweight tool to stat the depth coverage of target regions of BAM file(s).", }, }, { id: "modules/bamtools", data: { name: "Bamtools", summary: "Provides both a programmer's API and an end-user's toolkit for handling BAM files.", }, }, { id: "modules/bases2fastq", data: { name: "Bases2Fastq", summary: "Demultiplexes and converts Element AVITI base calls into FASTQ files." }, }, { id: "modules/bbduk", data: { name: "BBDuk", summary: "Common data-quality-related trimming, filtering, and masking operations with a kmer based approach.", }, }, { id: "modules/bbmap", data: { name: "BBTools", summary: "Pre-processing, assembly, alignment, and statistics tools for DNA/RNA sequencing reads.", }, }, { id: "modules/bcftools", data: { name: "Bcftools", summary: "Utilities for variant calling and manipulating VCFs and BCFs." }, }, { id: "modules/bcl2fastq", data: { name: "bcl2fastq", summary: "Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.", }, }, { id: "modules/bclconvert", data: { name: "BCL Convert", summary: "Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.", }, }, { id: "modules/biobambam2", data: { name: "biobambam2", summary: "Tools for early stage alignment file processing." }, }, { id: "modules/biobloomtools", data: { name: "BioBloom Tools", summary: "Assigns reads to different references using bloom filters. This is faster than alignment and can be used for contamination detection.", }, }, { id: "modules/biscuit", data: { name: "BISCUIT", summary: "Maps bisulfite converted DNA sequence reads and determines cytosine methylation states.", }, }, { id: "modules/bismark", data: { name: "Bismark", summary: "Maps bisulfite converted sequence reads and determine cytosine methylation states.", }, }, { id: "modules/bowtie1", data: { name: "Bowtie 1", summary: "Ultrafast, memory-efficient short read aligner." } }, { id: "modules/bowtie2", data: { name: "Bowtie 2 / HiSAT2", summary: "Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.", }, }, { id: "modules/busco", data: { name: "BUSCO", summary: "Assesses genome assembly and annotation completeness." } }, { id: "modules/bustools", data: { name: "Bustools", summary: "Tools for BUS files - a file format for single-cell RNA-seq data designed to facilitate the development of modular workflows for data processing.", }, }, { id: "modules/ccs", data: { name: "CCS", summary: "PacBio tool that generates highly accurate single-molecule consensus reads (HiFi Reads).", }, }, { id: "modules/cellranger", data: { name: "Cell Ranger", summary: "Analyzes single cell expression or VDJ data produced by 10X Genomics." }, }, { id: "modules/cellranger_arc", data: { name: "Cell Ranger ARC", summary: "Analyzes single-cell multiome ATAC and gene expression data produced by 10X Genomics.", }, }, { id: "modules/cells2stats", data: { name: "cells2stats", summary: "Generate output files and statistics from Element Biosciences Teton cytoprofiling assays.", }, }, { id: "modules/checkatlas", data: { name: "CheckAtlas", summary: "A one-liner tool for quality control of your single-cell atlases." }, }, { id: "modules/checkm", data: { name: "CheckM", summary: "Estimates genome completeness and contamination based on the presence or absence of marker genes.", }, }, { id: "modules/checkm2", data: { name: "CheckM2", summary: "Assesses microbial genome quality using machine learning." }, }, { id: "modules/checkqc", data: { name: "CheckQC", summary: "Checks a set of quality criteria against an Illumina runfolder." }, }, { id: "modules/clipandmerge", data: { name: "ClipAndMerge", summary: "Adapter clipping and read merging for ancient DNA data." }, }, { id: "modules/clusterflow", data: { name: "Cluster Flow", summary: "Simple and flexible bioinformatics pipeline tool." }, }, { id: "modules/conpair", data: { name: "Conpair", summary: "Estimates concordance and contamination for tumor\u2013normal pairs." }, }, { id: "modules/cutadapt", data: { name: "Cutadapt", summary: "Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.", }, }, { id: "modules/damageprofiler", data: { name: "DamageProfiler", summary: "DNA damage pattern retrieval for ancient DNA analysis." }, }, { id: "modules/deacon", data: { name: "Deacon", summary: "Search and depletion of FASTA/FASTQ files and streams using accelerated minimizer matching.", }, }, { id: "modules/dedup", data: { name: "DeDup", summary: "Improved Duplicate Removal for merged/collapsed reads in ancient DNA analysis.", }, }, { id: "modules/deeptools", data: { name: "deepTools", summary: "Tools to process and analyze deep sequencing data." }, }, { id: "modules/diamond", data: { name: "DIAMOND", summary: "Sequence aligner for protein and translated DNA searches, a drop-in replacement for the NCBI BLAST.", }, }, { id: "modules/disambiguate", data: { name: "Disambiguate", summary: "Disambiguate reads aligned to two different species (e.g. human and mouse).", }, }, { id: "modules/dragen", data: { name: "DRAGEN", summary: "Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.", }, }, { id: "modules/dragen_fastqc", data: { name: "DRAGEN-FastQC", summary: "Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.", }, }, { id: "modules/eigenstratdatabasetools", data: { name: "eigenstratdatabasetools", summary: "Tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.", }, }, { id: "modules/fastp", data: { name: "fastp", summary: "All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).", }, }, { id: "modules/fastq_screen", data: { name: "FastQ Screen", summary: "Screens a library of sequences in FastQ format against a set of sequence databases to see if the composition of the library matches with what you expect.", }, }, { id: "modules/fastqc", data: { name: "FastQC", summary: "Quality control tool for high throughput sequencing data." }, }, { id: "modules/fastqe", data: { name: "FastQE", summary: "Uses emoji to represent FASTQ sequence quality scores." }, }, { id: "modules/featurecounts", data: { name: "featureCounts", summary: "Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.", }, }, { id: "modules/fgbio", data: { name: "fgbio", summary: "Processing and evaluating data containing UMIs." } }, { id: "modules/filtlong", data: { name: "Filtlong", summary: "Filters long reads by quality." } }, { id: "modules/flash", data: { name: "FLASh", summary: "Merges paired-end reads from next-generation sequencing experiments." }, }, { id: "modules/flexbar", data: { name: "Flexbar", summary: "Barcode and adapter removal tool." } }, { id: "modules/freyja", data: { name: "Freyja", summary: "Recovers relative lineage abundances from mixed SARS-CoV-2 samples." }, }, { id: "modules/ganon", data: { name: "Ganon", summary: "Metagenomics classification: quickly assigns sequence fragments to their closest reference among thousands of references via Interleaved Bloom Filters of k-mer/minimizers.", }, }, { id: "modules/gatk", data: { name: "GATK", summary: "Wide variety of tools with a primary focus on variant discovery and genotyping.", }, }, { id: "modules/gffcompare", data: { name: "GffCompare", summary: "Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.", }, }, { id: "modules/glimpse", data: { name: "GLIMPSE", summary: "Low-coverage whole genome sequencing imputation." } }, { id: "modules/goleft_indexcov", data: { name: "goleft indexcov", summary: "Quickly estimate coverage from a whole-genome bam index, providing 16KB resolution.", }, }, { id: "modules/gopeaks", data: { name: "GoPeaks", summary: "Calls peaks in CUT&TAG/CUT&RUN datasets." } }, { id: "modules/gtdbtk", data: { name: "GTDB-Tk", summary: "Assigns objective taxonomic classifications to bacterial and archaeal genomes.", }, }, { id: "modules/haplocheck", data: { name: "Haplocheck", summary: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.", }, }, { id: "modules/happy", data: { name: "hap.py", summary: "Benchmarks variant calls against gold standard truth datasets." }, }, { id: "modules/hicexplorer", data: { name: "HiCExplorer", summary: "Hi-C analysis from processing to visualization." }, }, { id: "modules/hicpro", data: { name: "HiC-Pro", summary: "Pipeline for Hi-C data processing." } }, { id: "modules/hicstuff", data: { name: "hicstuff", summary: "Hi-C pipeline that generates contact maps from sequencing reads." }, }, { id: "modules/hicup", data: { name: "HiCUP", summary: "Mapping and quality control on Hi-C data." } }, { id: "modules/hifi_trimmer", data: { name: "HiFi-Trimmer", summary: "Filters and trims adapter sequences from HiFi reads using BLAST." }, }, { id: "modules/hifiasm", data: { name: "HiFiasm", summary: "Haplotype-resolved assembler for accurate Hifi reads." }, }, { id: "modules/hisat2", data: { name: "HISAT2", summary: "Maps DNA or RNA reads against a genome or a population of genomes." }, }, { id: "modules/homer", data: { name: "HOMER", summary: "Motif discovery and next-gen sequencing analysis." } }, { id: "modules/hops", data: { name: "HOPS", summary: "Ancient DNA characteristics screening tool of output from the metagenomic aligner MALT.", }, }, { id: "modules/hostile", data: { name: "Hostile", summary: "Removes host sequences from short and long read (meta)genomes, from paired or unpaired fastq[.gz].", }, }, { id: "modules/htseq", data: { name: "HTSeq Count", summary: "Part of the HTSeq package: counts reads covering specified genomic features.", }, }, { id: "modules/humid", data: { name: "HUMID", summary: "Reference-free tool to quickly remove duplicates from FastQ files, with or without UMIs.", }, }, { id: "modules/interop", data: { name: "Illumina InterOp Statistics", summary: "Reading and writing InterOp metric files." }, }, { id: "modules/isoseq", data: { name: "Iso-Seq", summary: "Identifies transcripts in PacBio single-molecule sequencing data (HiFi reads).", }, }, { id: "modules/ivar", data: { name: "iVar", summary: "Functions for viral amplicon-based sequencing." } }, { id: "modules/jcvi", data: { name: "JCVI Genome Annotation", summary: "Computes statistics on genome annotation." }, }, { id: "modules/jellyfish", data: { name: "Jellyfish", summary: "Counting k-mers in DNA." } }, { id: "modules/kaiju", data: { name: "Kaiju", summary: "Taxonomic classification for metagenomics." } }, { id: "modules/kallisto", data: { name: "Kallisto", summary: "Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data.", }, }, { id: "modules/kat", data: { name: "K-mer Analysis Toolkit", summary: "Analyses sequencing data via its k-mer spectra." }, }, { id: "modules/kraken", data: { name: "Kraken", summary: "Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.", }, }, { id: "modules/leehom", data: { name: "leeHom", summary: "Bayesian reconstruction of ancient DNA." } }, { id: "modules/librarian", data: { name: "Librarian", summary: "Predicts the sequencing library type from the base composition of a FastQ file.", }, }, { id: "modules/lima", data: { name: "Lima", summary: "Demultiplex PacBio single-molecule sequencing reads." } }, { id: "modules/longranger", data: { name: "Long Ranger", summary: "Sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling.", }, }, { id: "modules/macs2", data: { name: "MACS2", summary: "Identifies transcription factor binding sites in ChIP-seq data." }, }, { id: "modules/malt", data: { name: "MALT", summary: "Aligns of metagenomic reads to a database of reference sequences (such as NR, GenBank or Silva) and outputs a MEGAN RMA file.", }, }, { id: "modules/mapdamage", data: { name: "mapDamage", summary: "Tracks and quantifies damage patterns in ancient DNA sequences." }, }, { id: "modules/megahit", data: { name: "MEGAHIT", summary: "NGS read assembler." } }, { id: "modules/metaphlan", data: { name: "MetaPhlAn", summary: "Profiles the composition of microbial communities from metagenomic shotgun sequencing data.", }, }, { id: "modules/methurator", data: { name: "Methurator", summary: "Estimates sequencing saturation for reduced-representation bisulfite sequencing (RRBS) data.", }, }, { id: "modules/methylqa", data: { name: "methylQA", summary: "Methylation sequencing data quality assessment tool." }, }, { id: "modules/mgikit", data: { name: "mgikit", summary: "Demultiplexes FASTQ files from an MGI sequencing instrument." }, }, { id: "modules/minionqc", data: { name: "MinIONQC", summary: "Quality control for ONT (Oxford Nanopore) long reads." }, }, { id: "modules/mirtop", data: { name: "mirtop", summary: "Annotates miRNAs and isomiRs and compute general statistics in mirGFF3 format.", }, }, { id: "modules/mirtrace", data: { name: "miRTrace", summary: "Quality control for small RNA sequencing data." } }, { id: "modules/mosaicatcher", data: { name: "MosaiCatcher", summary: "Counts strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.", }, }, { id: "modules/mosdepth", data: { name: "Mosdepth", summary: "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing." }, }, { id: "modules/motus", data: { name: "Motus", summary: "Microbial profiling through marker gene (MG)-based operational taxonomic units (mOTUs).", }, }, { id: "modules/mtnucratio", data: { name: "mtnucratio", summary: "Computes mitochondrial to nuclear genome ratios in NGS datasets." }, }, { id: "modules/multivcfanalyzer", data: { name: "MultiVCFAnalyzer", summary: "Reads multiple VCF files into combined genotype calls, produces summary statistics and downstream formats.", }, }, { id: "modules/nanoq", data: { name: "nanoq", summary: "Reports read quality and length from nanopore sequencing data." }, }, { id: "modules/nanostat", data: { name: "NanoStat", summary: "Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).", }, }, { id: "modules/nextclade", data: { name: "Nextclade", summary: "Viral genome alignment, clade assignment, mutation calling, and quality checks.", }, }, { id: "modules/ngsbits", data: { name: "ngs-bits", summary: "Calculating statistics from FASTQ, BAM, and VCF." } }, { id: "modules/ngsderive", data: { name: "ngsderive", summary: "Forensic tool for by backwards computing library information in sequencing data.", }, }, { id: "modules/nonpareil", data: { name: "Nonpareil", summary: "Estimates metagenomic coverage and sequence diversity." }, }, { id: "modules/odgi", data: { name: "ODGI", summary: "Analysis and manipulation of pangenome graphs structured in the variation graph model.", }, }, { id: "modules/optitype", data: { name: "OptiType", summary: "Precision HLA typing from next-generation sequencing data." }, }, { id: "modules/pairtools", data: { name: "pairtools", summary: "Toolkit for Chromatin Conformation Capture experiments. Handles short-reads paired reference alignments, extracts 3C-specific information, and perform common tasks such as sorting, filtering, and deduplication.", }, }, { id: "modules/pangolin", data: { name: "Pangolin", summary: "Uses variant calls to assign SARS-CoV-2 genome sequences to global lineages.", }, }, { id: "modules/pbmarkdup", data: { name: "pbmarkdup", summary: "Takes one or multiple sequencing chips of an amplified libray as HiFi reads and marks or removes duplicates.", }, }, { id: "modules/peddy", data: { name: "Peddy", summary: "Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF.", }, }, { id: "modules/percolator", data: { name: "Percolator", summary: "Semi-supervised learning for peptide identification from shotgun proteomics datasets.", }, }, { id: "modules/phantompeakqualtools", data: { name: "phantompeakqualtools", summary: "Computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.", }, }, { id: "modules/picard", data: { name: "Picard", summary: "Tools for manipulating high-throughput sequencing data." }, }, { id: "modules/porechop", data: { name: "Porechop", summary: "Finds and removes adapters from Oxford Nanopore reads." }, }, { id: "modules/preseq", data: { name: "Preseq", summary: "Estimates library complexity, showing how many additional unique reads are sequenced for increasing total read count.", }, }, { id: "modules/prinseqplusplus", data: { name: "PRINSEQ++", summary: "C++ implementation of the prinseq-lite.pl program. Filters, reformats, and trims genomic and metagenomic reads.", }, }, { id: "modules/prokka", data: { name: "Prokka", summary: "Rapid annotation of prokaryotic genomes." } }, { id: "modules/purple", data: { name: "PURPLE", summary: "A purity, ploidy and copy number estimator for whole genome tumor data." }, }, { id: "modules/pychopper", data: { name: "Pychopper", summary: "Identifies, orients, trims and rescues full length Nanopore cDNA reads. Can also rescue fused reads.", }, }, { id: "modules/pycoqc", data: { name: "pycoQC", summary: "Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.", }, }, { id: "modules/qc3C", data: { name: "qc3C", summary: "Reference-free and BAM based quality control for Hi-C data." }, }, { id: "modules/qorts", data: { name: "QoRTs", summary: "Toolkit for analysis, QC, and data management of RNA-Seq datasets." }, }, { id: "modules/qualimap", data: { name: "QualiMap", summary: "Quality control of alignment data and its derivatives like feature counts." }, }, { id: "modules/quast", data: { name: "QUAST", summary: "Quality assessment tool for genome assemblies." } }, { id: "modules/ribotish", data: { name: "Ribo-TISH", summary: "Identifies translated ORFs from Ribo-seq data and reports reading frame quality metrics.", }, }, { id: "modules/ribowaltz", data: { name: "riboWaltz", summary: "Computes P-site offsets and performs quality control for ribosome profiling data.", }, }, { id: "modules/riker", data: { name: "Riker", summary: "Fast Rust toolkit that ports key sequencing QC tools from Picard." }, }, { id: "modules/rna_seqc", data: { name: "RNA-SeQC", summary: "RNA-Seq metrics for quality control and process optimization." }, }, { id: "modules/rockhopper", data: { name: "Rockhopper", summary: "Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs.", }, }, { id: "modules/rsem", data: { name: "RSEM", summary: "Estimates gene and isoform expression levels from RNA-Seq data." }, }, { id: "modules/rseqc", data: { name: "RSeQC", summary: "Evaluates high throughput RNA-seq data." } }, { id: "modules/salmon", data: { name: "Salmon", summary: "Quantifies expression of transcripts using RNA-seq data." }, }, { id: "modules/sambamba", data: { name: "Sambamba", summary: "Toolkit for interacting with BAM/CRAM files." } }, { id: "modules/samblaster", data: { name: "Samblaster", summary: "Marks duplicates and extracts discordant and split reads from sam files." }, }, { id: "modules/samtools", data: { name: "Samtools", summary: "Toolkit for interacting with BAM/CRAM files." } }, { id: "modules/sargasso", data: { name: "Sargasso", summary: "Separates mixed-species RNA-seq reads according to their species of origin.", }, }, { id: "modules/seqera_cli", data: { name: "Seqera Platform CLI", summary: "Reports statistics generated by the Seqera Platform CLI." }, }, { id: "modules/seqfu", data: { name: "Seqfu", summary: "Manipulate FASTA/FASTQ files." } }, { id: "modules/seqkit", data: { name: "SeqKit", summary: "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation." }, }, { id: "modules/sequali", data: { name: "Sequali", summary: "Sequencing quality control for both long-read and short-read data." }, }, { id: "modules/seqwho", data: { name: "SeqWho", summary: "Determines FASTQ(A) sequencing file source protocol and the species of origin, to check that the composition of the library is expected.", }, }, { id: "modules/seqyclean", data: { name: "SeqyClean", summary: "Filters adapters, vectors, and contaminants while quality trimming." }, }, { id: "modules/sexdeterrmine", data: { name: "SexDetErrmine", summary: "Calculates relative coverage of X and Y chromosomes and their associated error bars from the depth of coverage at specified SNPs.", }, }, { id: "modules/sickle", data: { name: "Sickle", summary: "A windowed adaptive trimming tool for FASTQ files using quality." }, }, { id: "modules/sincei", data: { name: "sincei", summary: "Toolkit for processing and analyzing single-cell (epi)genomics data." }, }, { id: "modules/skewer", data: { name: "Skewer", summary: "Adapter trimming tool for NGS paired-end sequences." } }, { id: "modules/slamdunk", data: { name: "Slamdunk", summary: "Tool to analyze SLAM-Seq data." } }, { id: "modules/snippy", data: { name: "Snippy", summary: "Rapid haploid variant calling and core genome alignment." }, }, { id: "modules/snpeff", data: { name: "SnpEff", summary: "Annotates and predicts the effects of variants on genes (such as amino acid changes).", }, }, { id: "modules/snpsplit", data: { name: "SNPsplit", summary: "Allele-specific alignment sorter. Determines allelic origin of reads that cover known SNP positions.", }, }, { id: "modules/somalier", data: { name: "Somalier", summary: "Genotype to pedigree correspondence checks from sketches derived from BAM/CRAM or VCF.", }, }, { id: "modules/sompy", data: { name: "som.py", summary: "Benchmarks somatic variant calls against gold standard truth datasets." }, }, { id: "modules/sortmerna", data: { name: "SortMeRNA", summary: "Program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.", }, }, { id: "modules/sourmash", data: { name: "Sourmash", summary: "Quickly searches, compares, and analyzes genomic and metagenomic data sets.", }, }, { id: "modules/spaceranger", data: { name: "Space Ranger", summary: "Tool to analyze 10x Genomics spatial transcriptomics data." }, }, { id: "modules/stacks", data: { name: "Stacks", summary: "Analyzes restriction enzyme-based data (e.g. RAD-seq)." }, }, { id: "modules/star", data: { name: "STAR", summary: "Universal RNA-seq aligner." } }, { id: "modules/supernova", data: { name: "Supernova", summary: "De novo genome assembler of 10X Genomics linked-reads." }, }, { id: "modules/sylphtax", data: { name: "Sylph-tax", summary: "Taxonomic profiling of metagenomic reads." } }, { id: "modules/telseq", data: { name: "telseq", summary: "Estimates telomere length from whole genome sequencing data (BAMs)." }, }, { id: "modules/theta2", data: { name: "THetA2", summary: "Estimates tumour purity and clonal / subclonal copy number." }, }, { id: "modules/tophat", data: { name: "Tophat", summary: "Splice junction RNA-Seq reads mapper for mammalian-sized genomes." }, }, { id: "modules/trim_galore", data: { name: "Trim Galore", summary: "Quality and adapter trimming for next-generation sequencing data, with special handling for RRBS libraries.", }, }, { id: "modules/trimmomatic", data: { name: "Trimmomatic", summary: "Read trimming tool for Illumina NGS data." } }, { id: "modules/truvari", data: { name: "Truvari", summary: "Benchmarking, merging, and annotating structural variants." }, }, { id: "modules/umicollapse", data: { name: "UMICollapse", summary: "Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.", }, }, { id: "modules/umitools", data: { name: "UMI-tools", summary: "Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes.", }, }, { id: "modules/varscan2", data: { name: "VarScan2", summary: "Variant detection in massively parallel sequencing data." }, }, { id: "modules/vcftools", data: { name: "VCFTools", summary: "Program to analyse and reporting on VCF files." } }, { id: "modules/vep", data: { name: "VEP", summary: "Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.", }, }, { id: "modules/verifybamid", data: { name: "VerifyBAMID", summary: "Detects sample contamination and/or sample swaps." }, }, { id: "modules/vg", data: { name: "VG", summary: "Toolkit to manipulate and analyze graphical genomes, including read alignment." }, }, { id: "modules/whatshap", data: { name: "WhatsHap", summary: "Phasing genomic variants using DNA reads (aka read-based phasing, or haplotype assembly).", }, }, { id: "modules/xengsort", data: { name: "Xengsort", summary: "Fast xenograft read sorter based on space-efficient k-mer hashing." }, }, { id: "modules/xenium", data: { name: "Xenium", summary: "Spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.", }, }, { id: "modules/xenome", data: { name: "Xenome", summary: "Classifies reads from xenograft sources." } }, ]} />