Browse Tools

Latch SDK — Python-native bioinformatics workflow platform for registering, executing, and sharing reproducible workflows on cloud infrastructure. Define workflows with @workflow and @task decorators,

Use when working with moveVis — an R package designed to visualize movement data (e.g., GPS tracking from animals or vehicles) and synchronous environmental data (e.g., remote sensing) through video a

Haploflow is a C++ de novo assembler for strain-resolved viral haplotype reconstruction from mixed quasispecies sequencing data. It applies minimum-flow decomposition on a de Bruijn graph to recover i

Use when working with matUtils — a toolkit for querying, interpreting, and manipulating mutation-annotated trees (MATs) in protobuf format. Part of the UShER project. Supports subcommands for tree sum

Use when working with odgi — the optimized dynamic genome/graph implementation toolkit — for pangenome variation graph manipulation, sorting, visualization, and analysis. Converts GFA graphs to effici

RepeatModeler — automated de novo repeat family identification and modeling pipeline for genomic sequences. Combines RECON and RepeatScout for consensus building, with optional LTR structural detectio

RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

SeqKit — cross-platform ultrafast toolkit for FASTA/Q file manipulation. 38 subcommands for sequence statistics (stats), filtering by length or quality (seq), pattern searching with mismatches (grep,

t-SNE (t-distributed Stochastic Neighbor Embedding) for nonlinear dimensionality reduction and visualization of high-dimensional data. Covers Barnes-Hut and exact modes, FIt-SNE/openTSNE interpolation

ThermoRawFileParser — cross-platform converter for Thermo Fisher RAW mass spectrometry files to open formats (mzML, MGF, Parquet). Supports batch conversion, metadata extraction, native peak picking,

Direct REST API access to UniProt (250M+ protein sequences, 570K+ reviewed Swiss-Prot entries). Protein search, FASTA/JSON retrieval, ID mapping across 200+ databases, batch retrieval, streaming, fiel

Use when working with UShER (Ultrafast Sample placement on Existing tRees) for phylogenetic placement of new samples onto existing mutation-annotated trees. Places sequences via maximum parsimony on l

Use when working with vg — the variation graph toolkit — for pangenome graph construction, read mapping to variation graphs, and graph-aware variant calling. Builds genome graphs from VCF + reference

Use when working with PolyFun — functionally-informed polygenic fine-mapping from GWAS summary statistics. Computes per-SNP heritability priors using S-LDSC with functional annotations, then runs SuSi

Use when working with poplddecay — popLDdecay — fast, memory-efficient

Use when working with SNeP — a tool for estimating effective population size (Ne) trajectories from genome-wide SNP linkage disequilibrium (LD) data. Reconstructs historical Ne by inverting the LD-Ne

COMETS (Computation Of Microbial Ecosystems in Time and Space) — dynamic flux balance analysis (dFBA) platform for simulating individual microbes and multi-species microbial communities in spatially-s

GRITS Toolbox is a free, open-source desktop application for processing, annotating, and archiving glycomics mass spectrometry data. It automates MS/MS spectral annotation of glycan fragments against

HyenaDNA long-context genomic foundation model workflows for sequence classification, embedding extraction, and long-range regulatory analysis. Includes checkpoint selection by context window (1k to 1

PDAL (Point Data Abstraction Library) — C/C++ toolkit for translating, filtering, and processing point cloud data from LiDAR, photogrammetry, and depth sensors. Provides JSON pipeline architecture wit

Nextstrain — an open-source project to harness the scientific and public health potential of pathogen genome data. Provides a continually-updated view of publicly available data alongside powerful ana

SEACells — single-cell metacell identification using kernel archetypal analysis. Aggregates highly similar single cells into metacells that preserve transcriptional and epigenomic heterogeneity while

The 'spocc' (Species Occurrence Data) R package provides a unified interface for querying and retrieving species occurrence data from multiple major biodiversity databases (GBIF, iNaturalist, eBird, O

SQANTI3 (Structural and Quality Annotation of Novel Transcript Isoforms) is a tool for the quality control, structural characterization, and curation of long-read defined transcriptomes. It classifies

Programmatic access to the U.S. EPA ToxCast and Tox21 high-throughput screening (HTS) bioactivity data via the CTX APIs. Use to query chemical hazard profiles, AC50 values, and hit-calls across thousa

xorca (eXtensible ORCA Grid Adapter) preprocesses NEMO ocean model NetCDF outputs into XGCM-compatible Xarray datasets for grid-aware operations on curvilinear ORCA grids. Use when working with NEMO s

estimate-compute-requirements — predict CPU, memory, wall time, and storage for bioinformatics pipelines given input data size and tool selection. Generates per-step resource tables, platform-specific

Use for deterministic conversion of workflow specifications into Nextflow DSL2, Snakemake 8+, WDL 1.0, and CWL v1.2 pipelines with container-aware resource routing and validation.

cftime — Python library for CF-convention date/time handling and non-standard calendar arithmetic. Decode and encode NetCDF time coordinates using num2date, date2num, num2pydate, date2index, and the c

Use when working with Nebulosa, the R/Bioconductor package for recovering single-cell gene expression signals via kernel density estimation (KDE). Covers plot_density(), weighted KDE (WKDE), joint den

NetCoMi (Network Construction and Comparison for Microbiome Data) — R package for constructing, analyzing, and comparing microbial association and dissimilarity networks from compositional count data.

Infernal — RNA covariance model (CM) toolkit for homology search and structural alignment of RNA sequences. Builds profile CMs from Stockholm alignments (cmbuild), calibrates E-values (cmcalibrate), s

MRtrix3 — open-source neuroimaging toolkit for diffusion MRI (dMRI) analysis, including DWI preprocessing, fiber orientation distribution (FOD) estimation, probabilistic and deterministic tractography

Look up documentation and code examples for bioinformatics tools using BioContext7

A Python library for verifying weather and climate forecasts.

ABySS — de novo genome assembler for short paired-end reads and genomes of all sizes. Uses Bloom filter mode for memory-efficient assembly (10x reduction vs hash table). Supports paired-end, mate-pair

Use when analyzing fMRI or MRI neuroimaging data with AFNI (Analysis of Functional NeuroImages). Covers full preprocessing pipelines, GLM-based activation analysis, group statistics, registration, sku

AGAT (Another Gff Analysis Toolkit) — comprehensive Perl toolkit for reading, writing, validating, fixing, and manipulating genome annotation files in GFF3, GTF, and GFF2 formats. Converts between for

Use when working with Aldy — a pharmacogenomics star-allele genotyper for pharmacogenes such as CYP2D6, CYP2C19, CYP2C9, DPYD, TPMT, G6PD, and others. Aldy detects allelic decomposition and performs e

alevin-fry — fast, accurate, and memory-frugal Rust-based tool for single-cell and single-nucleus RNA-seq quantification. Processes RAD (Reduced Alignment Data) files from salmon alevin to generate ce

AlphaPept — Python-based, open-source proteomics pipeline for DDA mass spectrometry data analysis. Provides feature detection, peptide identification via database search, deep learning-based scoring,

AlphaTims — open-source Python package for fast indexing, slicing, and visualization of unprocessed Bruker timsTOF Pro LC-TIMS-Q-TOF mass spectrometry data. Loads raw .d folders into a sparse five-dim

AnnotSV — integrated tool for structural variation annotation and ranking. Annotates DEL, DUP, INS, INV, and translocation SVs from VCF or BED input against 30+ databases (gnomAD-SV, DGV, ClinVar, OMI

Anvi'o — integrated analysis and visualization platform for 'omics data. Supports metagenomics (MAG binning, refinement, read recruitment), pangenomics (gene cluster analysis, ANI computation), phylog

Artemis and ACT (Artemis Comparison Tool) — Java-based genome browser and annotation suite from the Wellcome Sanger Institute for viewing, creating, and editing sequence features and annotations in EM

ascatNgs — allele-specific copy number analysis of tumour and matched normal whole-genome sequencing data. Implements the ASCAT algorithm for NGS data, estimating tumour purity, ploidy, and allele-spe

bamAlignCleaner — removes unaligned references from BAM/CRAM alignment files. Cleans alignment files by filtering out reference sequences with no mapped reads, reducing file size and speeding downstre