Browse Tools

Roary — rapid large-scale prokaryotic pan genome analysis. Calculates the pan genome from annotated assemblies (GFF3 from Prokka/Bakta), producing core and accessory gene clusters, gene presence/absen

Use when working with sage — sage — ultrafast Rust proteomics search

SAIGE — scalable genome-wide association tests in biobank-scale data using generalized mixed models with saddlepoint approximation. Fits null logistic/linear mixed models with sparse or full GRM to ac

salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s

SALSA2 — scaffold long-read genome assemblies using Hi-C proximity ligation data. Takes a draft contig assembly and Hi-C read alignments (BAM/BED) to produce chromosome-scale scaffolds. Iteratively co

Sambamba — high-performance BAM/CRAM processing tool written in D with native multi-threading. Provides fast sorting, indexing, duplicate marking, merging, filtering, depth calculation, flagstat, and

scib (single-cell integration benchmarking) -- Python framework for evaluating and benchmarking batch correction and data integration methods in single-cell omics. Computes standardized metrics for bi

Use when working with SciPy — the foundational Python scientific computing library — for statistical testing, signal processing, optimization, linear algebra, spatial analysis, and numerical integrati

SEACR (Sparse Enrichment Analysis for CUT&RUN) — peak caller specifically designed for CUT&RUN and CUT&Tag chromatin profiling data. Uses the sparse signal characteristics of CUT&RUN to call enriched

seqtk — fast lightweight C toolkit for processing FASTA and FASTQ files. Supports format conversion (FASTQ↔FASTA), random subsampling, quality trimming, reverse complement, base composition, sequence

Shasta — fast de novo long-read genome assembler optimized for Oxford Nanopore (ONT) reads. Produces haploid or phased diploid assemblies from nanopore data using run-length encoding, MinHash-based ov

sleuth — R package for differential expression analysis of RNA-seq data at the transcript level. Works with kallisto bootstrap quantifications to model technical variability using a response error mod

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

Use when working with SNAP (Scalable Nucleotide Alignment Program) — a fast DNA sequence aligner developed at UC Berkeley's AMPLab. Use for aligning short or long DNA reads to a reference genome, buil

SnapATAC2 — Python/Rust toolkit for single-cell ATAC-seq analysis. Provides fragment file import, cell-by-bin/peak matrix generation, spectral embedding dimensionality reduction, leiden clustering, MA

Sniffles2 — fast structural variant caller for long-read sequencing data (PacBio HiFi, Oxford Nanopore). Detects deletions, insertions, duplications, inversions, and translocations from BAM/CRAM align

SnpEff — fast Java-based variant annotation and effect prediction tool that annotates genomic variants (SNPs, indels, MNPs) with gene impact, protein changes, loss-of-function predictions, and HGVS no

SOAPdenovo2 — de novo short-read genome assembler for large plant and animal genomes using de Bruijn graph construction. Runs a four-stage pipeline: pregraph (k-mer graph), contig (initial contigs), m

SOAPnuke — C++ quality control and preprocessing tool for high-throughput sequencing data. Filters and trims paired-end or single-end FASTQ reads by adapter content, low quality bases, N-base ratio, r

SortMeRNA — fast filtering of ribosomal RNA reads from metatranscriptomic and RNA-seq data using local sequence alignment against curated rRNA databases (SILVA, RFAM). CLI tool for rRNA removal, rRNA

Souporcell — genotype-based demultiplexing of pooled single-cell RNA-seq experiments. Assigns cells to donor of origin using SNP variants from the aligned BAM file without requiring known genotypes. D

squigualiser is a Python tool for visualizing raw nanopore sequencing signal (squiggle) data aligned to reference sequences. Generates interactive HTML-based plots using Bokeh that overlay raw current

Stacks is a software pipeline for building loci from short-read sequencing data (RAD-seq, GBS, ddRAD, 2b-RAD) for population genomics and phylogeography. Supports de novo and reference-guided assembly

STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv

Use when working with STARR-seq (Self-Transcribing Active Regulatory Region sequencing) data analysis. STARRpeaker calls enhancer peaks from STARR-seq BAM files using negative binomial regression to a

Strelka2 — fast and accurate small variant caller for germline and somatic analysis. Detects SNVs and indels (up to ~49 bp) from mapped paired-end sequencing reads with tiered haplotype modeling, adap

SUPPA2 — fast, accurate analysis of alternative splicing from RNA-seq data. Calculates PSI (Percent Spliced In) values per event and per transcript from transcript quantification (Salmon, kallisto, RS

SURVIVOR — C++ toolkit for structural variation (SV) analysis including merging multi-caller VCF files into consensus callsets, SV simulation on reference genomes, benchmarking SV callers against trut

SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno

SVIM — structural variant identification from long-read sequencing data (PacBio, Oxford Nanopore). Detects deletions, insertions, tandem and interspersed duplications, inversions, and translocations f

Sylph — ultrafast metagenomic profiling and containment ANI estimation using k-mer sketching. Performs species-level taxonomic profiling with abundance quantification and genome querying against pre-b

Tandem Repeats Finder (TRF) — command-line tool for locating and displaying tandem repeats in DNA sequences. Detects microsatellites (STRs), minisatellites, and larger tandem duplications using a prob

Use when reconstructing T-cell receptor (TCR) or B-cell receptor (BCR) repertoires from bulk RNA-seq or single-cell RNA-seq data using TRUST4. Covers IMGT reference preparation, BAM/FASTQ input, CDR3

UNITE is the reference database and taxonomy system for fungal ITS (Internal Transcribed Spacer) metabarcoding and amplicon sequencing. Use for classifying fungal sequences against Species Hypotheses

USEARCH — ultra-fast amplicon sequence analysis toolkit for 16S/ITS/18S microbiome studies. Supports FASTQ quality filtering (fastq_filter), paired-end merging (fastq_mergepairs), dereplication (derep

VarScan2 -- Java-based variant caller for somatic and germline SNV/indel detection, copy number analysis, and LOH detection from samtools mpileup output. Supports tumor-normal paired somatic calling,

Velocyto — RNA velocity estimation tool that distinguishes unspliced and spliced mRNAs in single-cell RNA-seq data to predict future cell states. Provides a CLI for counting spliced/unspliced/ambiguou

VEP (Ensembl Variant Effect Predictor) — gold-standard tool for annotating and predicting the functional effects of genomic variants on genes, transcripts, and protein sequences. Provides consequence

Verkko — hybrid genome assembler for telomere-to-telomere (T2T) diploid assembly from PacBio HiFi and Oxford Nanopore ultra-long reads. Combines MBG de Bruijn graphs with progressive ONT resolution, t

VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering

vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,

Wengan — hybrid genome assembler combining short and long reads using a synthetic scaffolding approach. Integrates short-read assembly backends (Minia3, ABySS2, DiscovarDenovo) with long-read pseudo-a

WiggleTools — command-line toolkit for streaming arithmetic and set operations on genomic signal tracks stored in Wiggle, BigWig, BedGraph, and BAM/CRAM formats. Computes sums, means, products, log tr

wtdbg2 — ultrafast de novo long-read genome assembler using a fuzzy de Bruijn graph approach. Assembles PacBio (RSII, Sequel, CCS) and Oxford Nanopore reads without prior error correction. Two-step wo

Use when scaffolding genome assemblies with Hi-C chromatin contact data using YaHS (Yet Another Hi-C Scaffolding Tool). Covers Hi-C BAM preparation, contig scaffolding, AGP output, juicer_tools contac

cf-python is a Python library implementing the CF (Climate and Forecast) metadata conventions for reading, writing, and analysing Earth-science datasets stored in netCDF, Zarr, PP, and UM formats. Use

Navigate the EDAM ontology hierarchy, find compatible tools and data types, and check format compatibility

GTDB-Tk — toolkit for objective taxonomic classification of bacterial and archaeal genomes using the Genome Taxonomy Database (GTDB). Assigns taxonomy based on placement in reference trees inferred fr

VarDict variant caller for SNVs, MNVs, indels, complex variants, and structural variants from BAM files. Supports somatic paired tumor-normal calling and single-sample germline mode. Ultra-sensitive v

AnnData — annotated data matrices for single-cell and multi-omics analysis. Core data structure for the scverse ecosystem storing expression matrices (X) with observation metadata (obs), variable meta