Browse Tools

FMLRC2 — FM-index Long Read Corrector version 2, a Rust-based hybrid error correction tool for long reads (PacBio CLR, Oxford Nanopore) using Illumina short reads as a correction guide. Builds a compr

Use when working with fraggenescan — fragGeneScan -- gene prediction

FreeBayes -- Bayesian haplotype-based variant caller for short-read sequencing data. Detects SNPs, indels, MNPs, and complex variants from BAM/CRAM alignments against a reference genome. Uses literal

Use when processing or analyzing Magnetic Resonance Spectroscopy (MRS) data with FSL MRS. Covers spectral fitting, basis set generation, preprocessing, quantification, and quality control of 1H-MRS an

FusionCatcher — tool for detecting somatic fusion genes, translocations, and chimeric transcripts from RNA-seq data. Identifies known and novel gene fusions in tumor and normal samples using multiple

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

Use this skill for GATK-based DNA methylation and bisulfite sequencing workflows including WGBS preprocessing, base quality score recalibration for bisulfite data, duplicate marking of bisulfite reads

GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase

GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual

GEMMA (Genome-wide Efficient Mixed Model Association) — fast C++ tool for genome-wide association study (GWAS) analysis using linear mixed models (LMM). Computes genetic relatedness matrices (GRM/kins

GeMoMa (Gene Model Mapper) is a Java-based homology-driven gene prediction tool for eukaryotic genome annotation. Uses protein and CDS sequences from annotated reference species to predict gene models

geNomad — identify viruses and plasmids in metagenomic assemblies and isolate genomes using neural-network sequence embeddings and marker gene profiles. Classifies sequences as chromosome, plasmid, or

Use when working with gfatools — a lightweight C toolkit for GFA format manipulation — for viewing, converting, sorting, and validating Graphical Fragment Assembly (GFA) files. Provides subcommands fo

gff3sort is a fast command-line tool for sorting GFF3 annotation files so that parent features always appear before their child features, and features on the same sequence are ordered by start coordin

gffcompare -- Tool for comparing, merging, and annotating RNA-seq transcript assemblies against a reference annotation. Classifies each assembled transcript with a class code (=, c, j, u, x, i, p, r,

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

GLnexus — scalable gVCF merging and joint variant calling for cohort genomics. Merges per-sample gVCFs from DeepVariant or GATK HaplotypeCaller into a joint-called project-level BCF/VCF using an embed

Use when working with goleft — a collection of Go-based tools for fast

Gubbins — rapid phylogenetic analysis of recombinant bacterial whole genome sequences. Iteratively detects recombination hotspots with elevated SNP density while constructing clonal frame phylogenies.

GWAS Catalog tools (gwas-sumstats-tools) are EMBL-EBI utilities for reading, writing, validating, and formatting genome-wide association study (GWAS) summary statistics in the GWAS-SSF standard format

Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c

Herro — haplotype-aware error correction for Oxford Nanopore long reads using deep learning. Corrects ONT simplex reads to Q30+ accuracy while preserving haplotype information for diploid assembly. Us

HiCanu — HiFi-optimized mode of the Canu genome assembler for accurate

HiCExplorer — comprehensive toolkit for Hi-C chromosome conformation capture data analysis, quality control, normalization, and visualization. Provides hicBuildMatrix (contact matrix construction), hi

HTSeq — Python framework for high-throughput sequencing data analysis, primarily used for counting aligned reads overlapping genomic features (genes, exons) from SAM/BAM/CRAM files using GTF/GFF annot

ICGC/ARGO tools — suite of command-line clients and APIs for accessing the International Cancer Genome Consortium (ICGC) and ARGO (Accelerating Research in Genomic Oncology) platform. Includes score-c

ipyrad is a Python toolkit for de novo and reference-guided assembly and genotyping of RADseq, GBS, ddRAD, 2bRAD, and other restriction enzyme-based reduced representation genomic datasets. Implements

Juicebox — interactive visualization and analysis tool for Hi-C and other proximity-ligation chromatin conformation data. Loads .hic files produced by Juicer, Dovetail, or Arima workflows and enables

kb-python — Python wrapper for the kallisto|bustools (kb) workflow for single-cell RNA-seq pre-processing. Runs kb ref to build or download reference indices and kb count to generate count matrices fr

KING — robust kinship estimation and relationship inference for genome-wide SNP data. Computes pairwise kinship coefficients, infers family relationships (MZ twins, parent-offspring, full siblings, 2n

Use when working with kmcp — KMCP — coverage-based metagenomic sequence

KneadData — quality control and host decontamination tool for metagenomic

Kraken 2 — fast k-mer-based taxonomic sequence classifier for metagenomics. Assigns NCBI taxonomic labels to DNA/protein sequences using exact k-mer matching against a minimizer-indexed hash table. Su

Krona — interactive HTML pie chart visualization of hierarchical taxonomic data from metagenomics and sequence classification. Part of KronaTools, which provides importers for Kraken2, BLAST, Diamond,

LAST — adaptive-seed sequence aligner for genomes, long reads, and proteins. Uses lastdb to build databases, last-train to learn substitution/gap rates, lastal for alignment, last-split for rearrangem

Liftoff — accurate genome annotation liftover tool that maps GFF/GTF annotations between assemblies of the same or closely-related species using Minimap2 alignment. Supports gene copy detection, ORF v

LINX — structural variant annotation and visualization tool from the Hartwig Medical Foundation hmftools suite. Interprets structural variants and copy number data to classify driver events including

locfdr — Efron's empirical Bayes local false discovery rate estimation from z-score vectors. Computes per-test posterior probability of being null using a mixture model approach that fits the empirica

LocusZoom — regional association plot generator for GWAS and fine-mapping results. Creates publication-quality locus zoom plots showing -log10(p-value) vs genomic position with LD coloring, recombinat

LSHTM PathogenSeq bioinformatics pipelines for pathogen whole-genome sequencing analysis, including TB-Profiler for Mycobacterium tuberculosis lineage and drug-resistance prediction from WGS data, Mal

LUMPY — probabilistic structural variant discovery from paired-end short-read sequencing. Detects deletions, duplications, inversions, and translocations from BWA-MEM aligned BAM files using discordan

MaAsLin 2 (Microbiome Multivariable Association with Linear Models 2) is the bioBakery tool for finding associations between microbial features (taxa, functional pathways, gene families) and sample me

MACS2/MACS3 — Model-based Analysis of ChIP-Seq for identifying transcription factor binding sites and histone modification enrichment from ChIP-seq, ATAC-seq, and CUT&Tag data. Provides peak calling (

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Knockout) -- computational pipeline for CRISPR genetic screen analysis. Performs sgRNA counting from FASTQ files (mageck count), gene-level essential

MAGeCK-VISPR — comprehensive CRISPR screen analysis framework combining MAGeCK statistical testing (RRA and MLE algorithms) with VISPR interactive visualization. Supports sgRNA count generation from F

MAJIQ — Modeling Alternative Junction Inclusion Quantification for detecting, quantifying, and visualizing local splicing variations (LSVs) from RNA-Seq data. Builds splice graphs from BAM files and G

MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit

Mash — fast genome and metagenome distance estimation using MinHash sketching. Estimates pairwise distances between genomic sequences (FASTA/FASTQ) without full alignment using k-mer sketches. Support

Mashtree — rapid distance-based phylogenetic tree construction from genome assemblies using MinHash (Mash) distances. Creates neighbor-joining trees from FASTA assemblies, FASTQ reads, or GenBank file

MaSuRCA (Maryland Super-Read Celera Assembler) — hybrid genome assembler combining Illumina short reads with PacBio or Oxford Nanopore long reads using super-read and mega-read technology. Performs au