Browse Tools

BAMtools — C++ API and command-line toolkit for reading, writing, sorting, indexing, filtering, merging, splitting, and converting BAM alignment files. Provides JSON-based filter expressions, multi-fo

bamutil — C++ toolkit for reading, writing, and manipulating BAM alignment files. Provides duplicate marking (dedup), base quality score recalibration (recab), overlapping read clipping (clipOverlap),

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) — interactive visualization tool for de novo assembly graphs in GFA and FASTG formats. Visualize genome assembly gr

BBDuk (Decontamination Using Kmers) — high-performance Java tool from the BBTools suite for adapter trimming, quality trimming, contaminant filtering, sequence masking, GC filtering, and format conver

BBKNN (Batch Balanced K Nearest Neighbours) -- lightweight Python batch correction method for single-cell RNA-seq that operates on the k-nearest neighbor graph rather than the expression matrix. Repla

BBMap/BBTools — suite of 265+ fast, multithreaded Java-based bioinformatics tools for DNA/RNA sequence analysis. Includes BBMap short read aligner, BBDuk adapter trimmer and quality filter, BBMerge pa

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format, demultiplexing sequencing runs by index sequences, or trimming adapters from short-read data. Handles HiSeq, MiSeq, NextSeq,

BEDOPS — high-performance genomic interval arithmetic suite for BED, VCF, GFF, GTF, BAM, and SAM files. Provides set operations (intersection, union, difference, complement, symmetric difference) via

bedToBigBed — UCSC Kent utility that converts BED/BED+ text files into indexed binary BigBed (.bb) format for fast random-access genome browser tracks. Supports BED3 through BED12, BED+N extra-field e

Use when building, querying, or manipulating colored compacted de Bruijn graphs (ccDBG) with Bifrost for genome assembly, metagenomics, variant detection, or k-mer analysis. Covers graph construction

bigWigMerge merges multiple bigWig signal tracks into a single bedGraph output by summing (or optionally taking the maximum of) per-base signal values. Essential for combining ChIP-seq, ATAC-seq, RNA-

biobambam2 — C++ toolkit for early-stage BAM file processing built on libmaus2. Provides bamsormadup for parallel sorting with duplicate marking, bamcollate2 for name-collation, bammarkduplicates for

BLASR (Basic Local Alignment with Successive Refinement) — PacBio long-read aligner for mapping SMRT sequencing reads to reference genomes. Uses suffix array indexing and global chaining for seed-and-

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

BRAKER — fully automated gene structure annotation pipeline combining GeneMark-ES/ET/EP/ETP with AUGUSTUS training. Supports RNA-Seq evidence (BRAKER1), protein evidence (BRAKER2), and combined RNA-Se

Use when working with bsseeker2 — BSseeker2 — bisulfite sequencing aligner

BUSCO (Benchmarking Universal Single-Copy Orthologs) — assess genome assembly, transcriptome, and proteome completeness using lineage-specific single-copy orthologs from the OrthoDB database. Reports

BUStools — C toolkit for manipulating BUS (Barcode, UMI, Set) files from single-cell RNA-seq pseudoalignment. Provides sorting, barcode error correction, UMI counting, matrix generation, quality inspe

BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace

BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace

Canu — long-read de novo genome assembler for PacBio HiFi, PacBio CLR, and Oxford Nanopore reads. Performs read correction, trimming, and overlap-layout-consensus assembly in three stages. Supports di

CD-HIT — fast sequence clustering and redundancy reduction for protein and nucleotide sequences. Clusters FASTA sequences at a user-defined identity threshold to remove redundancy from databases. Prov

ChAMP — Chip Analysis Methylation Pipeline for Illumina 450K and EPIC arrays. Integrated R/Bioconductor pipeline for DNA methylation analysis covering IDAT loading, quality control, normalization (BMI

Chromosight — Python computer-vision tool for detecting chromatin loops, borders (TAD boundaries), hairpins, and other patterns in Hi-C contact maps using template matching with Pearson correlation. R

chromVAR — R/Bioconductor package for determining variation in chromatin accessibility across sets of annotations or peaks. Designed for single-cell ATAC-seq (scATAC-seq) and sparse bulk ATAC-seq data

Circos — Perl-based circular visualization tool for genomics data. Creates publication-quality circular plots for genome comparisons, synteny, GC content, gene density, chromosome ideograms, link/ribb

CNVkit -- Python toolkit for detecting copy number variants (CNVs) from targeted DNA sequencing data (hybrid capture, amplicon) and whole-genome sequencing (WGS). Leverages both on-target and off-targ

CONCOCT — metagenomic binning tool that clusters contigs into genomes using sequence composition (k-mer frequencies) and coverage across multiple samples. Combines PCA dimensionality reduction with Ga

cooler — file format and Python library for Hi-C chromatin contact data. Stores sparse contact matrices in .cool (single-resolution) and .mcool (multi-resolution) HDF5 files. Supports ingestion from p

Use when working with cramino — a fast QC tool for long-read alignment files (CRAM and BAM). Generates alignment statistics including N50, median length, mean quality, percent aligned, and yield from

Use when working with csvtk — csvtk — cross-platform, ultrafast CSV/TSV

Cufflinks — RNA-seq transcript assembly, quantification, and differential expression suite. Assembles aligned reads into transcripts (cufflinks), performs differential expression analysis at transcrip

DADA2 — high-resolution amplicon sequence variant (ASV) inference from Illumina, 454, and Ion Torrent amplicon sequencing data. R/Bioconductor package that models sequencing errors to resolve exact bi

DAS Tool — genome-resolved metagenomics bin refinement tool that integrates results from multiple binning algorithms to produce an optimized, non-redundant set of metagenome-assembled genomes (MAGs).

Use when working with datamash — datamash — GNU command-line tool for

DeepVariant — CNN-based variant caller that converts aligned reads into pileup image tensors and classifies them with a deep neural network to produce SNP and indel calls in VCF/gVCF format. Supports

dnaPipeTE (do not assemble - PipelinE for Transposable Elements) is a bioinformatics pipeline for estimating the proportion and landscape of transposable elements (TEs) and other repeats in a genome f

DRAGMAP — Illumina's open-source hash-table-based DNA short-read aligner, implementing the DRAGEN mapping algorithm. Produces SAM/BAM output from FASTQ inputs against a pre-built hash table index. Use

DRAM-v (Distilled and Refined Annotation of Metabolism — Viral) — annotate viral genomes and metagenome-assembled phage sequences for auxiliary metabolic genes (AMGs) and viral hallmarks. Produces ann

DRIMSeq is a Bioconductor R package for Differential Transcript Usage (DTU) analysis using a Dirichlet-multinomial distribution to model transcript-level count proportions. Tests whether relative tran

Dysgu — structural variant caller for paired-end and long-read sequencing data (Illumina, PacBio HiFi, Oxford Nanopore). Detects deletions, insertions, duplications, inversions, and translocations fro

Use when detecting allele-specific expression (ASE), allelic imbalance, or phased allele counts from RNA-seq data with EAGLE (Empirical Analysis of Allele-Specific Gene Expression). Covers phased VCF

Use when processing EEG or MEG data with EEGLAB (MATLAB toolbox). Covers loading raw data, filtering, re-referencing, epoching, ICA, artifact rejection, channel interpolation, time-frequency analysis,

EIGENSOFT smartpca -- C/C++ tool for principal component analysis of genome-wide SNP genotype data. Computes eigenvectors and eigenvalues for population structure analysis, ancestry inference, stratif

EMU (Exact Mapping-based Unambiguous) — species-level 16S rRNA taxonomic profiling for long-read sequencing data (Oxford Nanopore, PacBio). Uses an expectation-maximization algorithm to resolve multi-

FACETS (Fraction and Allele-Specific Copy number Estimates from Tumor/normal Sequencing) is an R package for allele-specific somatic copy number analysis of matched tumor-normal sequencing data. It es

Fastq Screen — Perl tool for screening FASTQ sequencing reads against multiple reference genomes to detect sample contamination. Maps reads to user-defined genome databases (human, mouse, E. coli, Phi

FastQC — universal quality control tool for high-throughput sequencing data. Performs modular analysis of FASTQ and BAM files, generating per-base quality scores, GC content distribution, adapter cont

featureCounts — ultrafast read counting program for assigning aligned reads (SAM/BAM) to genomic features such as genes, exons, promoters, and genomic bins. Part of the Subread package. Supports singl

fgbio — command-line toolkit for working with genomic and next-generation sequencing data, specializing in UMI (Unique Molecular Identifier) processing, consensus read calling, duplex sequencing, and