Adapter Removal
<p>Removes adapter sequences, trims low quality bases from 3' ends, or merges overlapping pairs into consensus.</p>
AfterQC
<p>Automatic filtering, trimming, error removing, and quality control for FastQ data.</p>
Anglerfish
<p>Quality controls Illumina libraries sequenced on Oxford Nanopore flowcells.</p>
ATAQV
<p>Toolkit for quality control and visualization of ATAC-seq data.</p>
Bakta
<p>Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.</p>
Bamdst
<p>Lightweight tool to stat the depth coverage of target regions of BAM file(s).</p>
Bamtools
<p>Provides both a programmer's API and an end-user's toolkit for handling BAM files.</p>
Bases2Fastq
<p>Demultiplexes and converts Element AVITI base calls into FASTQ files.</p>
BBDuk
<p>Common data-quality-related trimming, filtering, and masking operations with a kmer based approach.</p>
BBTools
<p>Pre-processing, assembly, alignment, and statistics tools for DNA/RNA sequencing reads.</p>
Bcftools
<p>Utilities for variant calling and manipulating VCFs and BCFs.</p>
bcl2fastq
<p>Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.</p>
BCL Convert
<p>Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.</p>
biobambam2
<p>Tools for early stage alignment file processing.</p>
BioBloom Tools
<p>Assigns reads to different references using bloom filters. This is faster than alignment and can be used for contamination detection.</p>
BISCUIT
<p>Maps bisulfite converted DNA sequence reads and determines cytosine methylation states.</p>
Bismark
<p>Maps bisulfite converted sequence reads and determine cytosine methylation states.</p>
Bowtie 1
<p>Ultrafast, memory-efficient short read aligner.</p>
Bowtie 2 / HiSAT2
<p>Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.</p>
BUSCO
<p>Assesses genome assembly and annotation completeness.</p>
Bustools
<p>Tools for BUS files - a file format for single-cell RNA-seq data designed to facilitate the development of modular workflows for data processing.</p>
CCS
<p>PacBio tool that generates highly accurate single-molecule consensus reads (HiFi Reads).</p>
Cell Ranger
<p>Analyzes single cell expression or VDJ data produced by 10X Genomics.</p>
Cell Ranger ARC
<p>Analyzes single-cell multiome ATAC and gene expression data produced by 10X Genomics.</p>
cells2stats
<p>Generate output files and statistics from Element Biosciences Teton cytoprofiling assays.</p>
CheckM
<p>Estimates genome completeness and contamination based on the presence or absence of marker genes.</p>
CheckM2
<p>Assesses microbial genome quality using machine learning.</p>
CheckQC
<p>Checks a set of quality criteria against an Illumina runfolder.</p>
ClipAndMerge
<p>Adapter clipping and read merging for ancient DNA data.</p>
Cluster Flow
<p>Simple and flexible bioinformatics pipeline tool.</p>
Conpair
<p>Estimates concordance and contamination for tumor–normal pairs.</p>
Cutadapt
<p>Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.</p>
DamageProfiler
<p>DNA damage pattern retrieval for ancient DNA analysis.</p>
DeDup
<p>Improved Duplicate Removal for merged/collapsed reads in ancient DNA analysis.</p>
deepTools
<p>Tools to process and analyze deep sequencing data.</p>
DIAMOND
<p>Sequence aligner for protein and translated DNA searches, a drop-in replacement for the NCBI BLAST.</p>
Disambiguate
<p>Disambiguate reads aligned to two different species (e.g. human and mouse).</p>
DRAGEN
<p>Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.</p>
DRAGEN-FastQC
<p>Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.</p>
eigenstratdatabasetools
<p>Tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.</p>
fastp
<p>All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).</p>
FastQ Screen
<p>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.</p>
FastQC
<p>Quality control tool for high throughput sequencing data.</p>
featureCounts
<p>Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.</p>
fgbio
<p>Processing and evaluating data containing UMIs.</p>
Filtlong
<p>Filters long reads by quality.</p>
FLASh
<p>Merges paired-end reads from next-generation sequencing experiments.</p>
Flexbar
<p>Barcode and adapter removal tool.</p>
Freyja
<p>Recovers relative lineage abundances from mixed SARS-CoV-2 samples.</p>
Ganon
<p>Metagenomics classification: quickly assigns sequence fragments to their closest reference among thousands of references via Interleaved Bloom Filters of k-mer/minimizers.</p>
GATK
<p>Wide variety of tools with a primary focus on variant discovery and genotyping.</p>
GffCompare
<p>Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.</p>
GLIMPSE
<p>Low-coverage whole genome sequencing imputation.</p>
goleft indexcov
<p>Quickly estimate coverage from a whole-genome bam index, providing 16KB resolution.</p>
GoPeaks
<p>Calls peaks in CUT&TAG/CUT&RUN datasets.</p>
GTDB-Tk
<p>Assigns objective taxonomic classifications to bacterial and archaeal genomes.</p>
Haplocheck
<p>Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.</p>
hap.py
<p>Benchmarks variant calls against gold standard truth datasets.</p>
HiCExplorer
<p>Hi-C analysis from processing to visualization.</p>
HiC-Pro
<p>Pipeline for Hi-C data processing.</p>
HiCUP
<p>Mapping and quality control on Hi-C data.</p>
HiFiasm
<p>Haplotype-resolved assembler for accurate Hifi reads.</p>
HISAT2
<p>Maps DNA or RNA reads against a genome or a population of genomes.</p>
HOMER
<p>Motif discovery and next-gen sequencing analysis.</p>
HOPS
<p>Ancient DNA characteristics screening tool of output from the metagenomic aligner MALT.</p>
Hostile
<p>Removes host sequences from short and long read (meta)genomes, from paired or unpaired fastq[.gz].</p>
HTSeq Count
<p>Part of the HTSeq package: counts reads covering specified genomic features.</p>
HUMID
<p>Reference-free tool to quickly remove duplicates from FastQ files, with or without UMIs.</p>
Iso-Seq
<p>Identifies transcripts in PacBio single-molecule sequencing data (HiFi reads).</p>
iVar
<p>Functions for viral amplicon-based sequencing.</p>
Kaiju
<p>Taxonomic classification for metagenomics.</p>
Kallisto
<p>Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data.</p>
Kraken
<p>Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.</p>
leeHom
<p>Bayesian reconstruction of ancient DNA.</p>
Librarian
<p>Predicts the sequencing library type from the base composition of a FastQ file.</p>
Lima
<p>Demultiplex PacBio single-molecule sequencing reads.</p>
Long Ranger
<p>Sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling.</p>
MACS2
<p>Identifies transcription factor binding sites in ChIP-seq data.</p>
MALT
<p>Aligns of metagenomic reads to a database of reference sequences (such as NR, GenBank or Silva) and outputs a MEGAN RMA file.</p>
mapDamage
<p>Tracks and quantifies damage patterns in ancient DNA sequences.</p>
MetaPhlAn
<p>Profiles the composition of microbial communities from metagenomic shotgun sequencing data.</p>
methylQA
<p>Methylation sequencing data quality assessment tool.</p>
mgikit
<p>Demultiplexes FASTQ files from an MGI sequencing instrument.</p>
MinIONQC
<p>Quality control for ONT (Oxford Nanopore) long reads.</p>
mirtop
<p>Annotates miRNAs and isomiRs and compute general statistics in mirGFF3 format.</p>
miRTrace
<p>Quality control for small RNA sequencing data.</p>
MosaiCatcher
<p>Counts strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.</p>
Mosdepth
<p>Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.</p>
Motus
<p>Microbial profiling through marker gene (MG)-based operational taxonomic units (mOTUs).</p>
mtnucratio
<p>Computes mitochondrial to nuclear genome ratios in NGS datasets.</p>
MultiVCFAnalyzer
<p>Reads multiple VCF files into combined genotype calls, produces summary statistics and downstream formats.</p>
nanoq
<p>Reports read quality and length from nanopore sequencing data.</p>
NanoStat
<p>Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).</p>
Nextclade
<p>Viral genome alignment, clade assignment, mutation calling, and quality checks.</p>
ngs-bits
<p>Calculating statistics from FASTQ, BAM, and VCF.</p>
ngsderive
<p>Forensic tool for by backwards computing library information in sequencing data.</p>
Nonpareil
<p>Estimates metagenomic coverage and sequence diversity.</p>
ODGI
<p>Analysis and manipulation of pangenome graphs structured in the variation graph model.</p>
OptiType
<p>Precision HLA typing from next-generation sequencing data.</p>
pairtools
<p>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.</p>
Pangolin
<p>Uses variant calls to assign SARS-CoV-2 genome sequences to global lineages.</p>
pbmarkdup
<p>Takes one or multiple sequencing chips of an amplified libray as HiFi reads and marks or removes duplicates.</p>
Peddy
<p>Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF.</p>
Percolator
<p>Semi-supervised learning for peptide identification from shotgun proteomics datasets.</p>
phantompeakqualtools
<p>Computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.</p>
Picard
<p>Tools for manipulating high-throughput sequencing data.</p>
Porechop
<p>Finds and removes adapters from Oxford Nanopore reads.</p>
Preseq
<p>Estimates library complexity, showing how many additional unique reads are sequenced for increasing total read count.</p>
PRINSEQ++
<p>C++ implementation of the prinseq-lite.pl program. Filters, reformats, and trims genomic and metagenomic reads.</p>
Prokka
<p>Rapid annotation of prokaryotic genomes.</p>
PURPLE
<p>A purity, ploidy and copy number estimator for whole genome tumor data.</p>
Pychopper
<p>Identifies, orients, trims and rescues full length Nanopore cDNA reads. Can also rescue fused reads.</p>
pycoQC
<p>Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.</p>
qc3C
<p>Reference-free and BAM based quality control for Hi-C data.</p>
QoRTs
<p>Toolkit for analysis, QC, and data management of RNA-Seq datasets.</p>
QualiMap
<p>Quality control of alignment data and its derivatives like feature counts.</p>
QUAST
<p>Quality assessment tool for genome assemblies.</p>
RNA-SeQC
<p>RNA-Seq metrics for quality control and process optimization.</p>
Rockhopper
<p>Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs.</p>
RSEM
<p>Estimates gene and isoform expression levels from RNA-Seq data.</p>
RSeQC
<p>Evaluates high throughput RNA-seq data.</p>
Salmon
<p>Quantifies expression of transcripts using RNA-seq data.</p>
Sambamba
<p>Toolkit for interacting with BAM/CRAM files.</p>
Samblaster
<p>Marks duplicates and extracts discordant and split reads from sam files.</p>
Samtools
<p>Toolkit for interacting with BAM/CRAM files.</p>
Sargasso
<p>Separates mixed-species RNA-seq reads according to their species of origin.</p>
Seqfu
<p>Manipulate FASTA/FASTQ files.</p>
Sequali
<p>Sequencing quality control for both long-read and short-read data.</p>
SeqWho
<p>Determines FASTQ(A) sequencing file source protocol and the species of origin, to check that the composition of the library is expected.</p>
SeqyClean
<p>Filters adapters, vectors, and contaminants while quality trimming.</p>
SexDetErrmine
<p>Calculates relative coverage of X and Y chromosomes and their associated error bars from the depth of coverage at specified SNPs.</p>
Sickle
<p>A windowed adaptive trimming tool for FASTQ files using quality.</p>
Skewer
<p>Adapter trimming tool for NGS paired-end sequences.</p>
Slamdunk
<p>Tool to analyze SLAM-Seq data.</p>
Snippy
<p>Rapid haploid variant calling and core genome alignment.</p>
SnpEff
<p>Annotates and predicts the effects of variants on genes (such as amino acid changes).</p>
SNPsplit
<p>Allele-specific alignment sorter. Determines allelic origin of reads that cover known SNP positions.</p>
Somalier
<p>Genotype to pedigree correspondence checks from sketches derived from BAM/CRAM or VCF.</p>
SortMeRNA
<p>Program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.</p>
Sourmash
<p>Quickly searches, compares, and analyzes genomic and metagenomic data sets.</p>
Space Ranger
<p>Tool to analyze 10x Genomics spatial transcriptomics data.</p>
Stacks
<p>Analyzes restriction enzyme-based data (e.g. RAD-seq).</p>
STAR
<p>Universal RNA-seq aligner.</p>
Supernova
<p>De novo genome assembler of 10X Genomics linked-reads.</p>
telseq
<p>Estimates telomere length from whole genome sequencing data (BAMs).</p>
THetA2
<p>Estimates tumour purity and clonal / subclonal copy number.</p>
Tophat
<p>Splice junction RNA-Seq reads mapper for mammalian-sized genomes.</p>
Trimmomatic
<p>Read trimming tool for Illumina NGS data.</p>
Truvari
<p>Benchmarking, merging, and annotating structural variants.</p>
UMICollapse
<p>Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.</p>
UMI-tools
<p>Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes.</p>
VarScan2
<p>Variant detection in massively parallel sequencing data.</p>
VCFTools
<p>Program to analyse and reporting on VCF files.</p>
VEP
<p>Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.</p>
VerifyBAMID
<p>Detects sample contamination and/or sample swaps.</p>
VG
<p>Toolkit to manipulate and analyze graphical genomes, including read alignment.</p>
WhatsHap
<p>Phasing genomic variants using DNA reads (aka read-based phasing, or haplotype assembly).</p>
Xengsort
<p>Fast xenograft read sorter based on space-efficient k-mer hashing.</p>
Xenium
<p>Spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.</p>
Xenome
<p>Classifies reads from xenograft sources.</p>
