Browse Tools

pbsv — PacBio structural variant (SV) caller for HiFi and CLR long-read sequencing data. Discovers and genotypes deletions, insertions, duplications, inversions, translocations, and breakends from ali

PGGB (PanGenome Graph Builder) — constructs unbiased pangenome variation graphs from multiple whole-genome assemblies using all-vs-all pairwise alignment (wfmash), graph induction (seqwish), and graph

PGS Catalog utilities — download, validate, match, and calculate polygenic scores (PGS) from the PGS Catalog database. Provides CLI tools for fetching scoring files by PGS ID or trait, combining multi

PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding) — dimensionality reduction for visualizing high-dimensional biological data while preserving both local and global structure

phyloseq -- R/Bioconductor package for importing, storing, analyzing, and visualizing microbiome census data. Handles OTU/ASV tables, taxonomy tables, sample metadata, phylogenetic trees, and referenc

PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2) predicts functional composition of microbial metagenomes from 16S rRNA, ITS1, or ITS2 amplicon marker gene

PLINK 2.0 — whole-genome association analysis toolset for large-scale genotype data management, quality control (missingness, HWE, MAF filtering), population stratification correction (PCA), linkage d

Use when building pangenome graphs or analyzing pangenome structure across prokaryotic genomes. PPanGGOLiN partitions gene families into persistent, shell, and cloud categories using a statistical mod

Preseq — C++ toolkit for predicting library complexity and future sequencing yield from genomic sequencing experiments. Estimates distinct molecule counts, extrapolates coverage curves, and identifies

pyBigWig is a Python library for reading and writing bigWig and bigBed files, the standard binary genome-browser signal formats. Use when users need to query per-base coverage or signal values from bi

RDP (Ribosomal Database Project) — curated 16S rRNA, 28S rRNA, and ITS fungal sequence database with integrated classification, alignment, and probe-matching tools. The RDP Classifier assigns taxonomy

Use when working with ribosome profiling (Ribo-seq) data to identify actively translated open reading frames (ORFs) using RiboCode — a Python tool for de novo ORF annotation from ribosome footprinting

Use when working with ribosome profiling (Ribo-seq) data and ORF discovery using Ribo-TISH — a Python toolkit for genome-wide identification and differential analysis of translational initiation. Cove

rMATS (Replicate Multivariate Analysis of Transcript Splicing) — statistical tool for detecting differential alternative splicing from RNA-seq data. Identifies five splicing event types: skipped exon

SAIGE-GENE+ — gene-based and region-based rare variant association testing using mixed models. Extends SAIGE to aggregate rare variants (SKAT, Burden, SKAT-O) while controlling for population structur

Sambamba mkdup routes duplicate-marking workflows for coordinate-sorted BAM files using `sambamba markdup`. Use this skill when a user needs to mark or remove duplicate reads, tune `--hash-table-size`

Use when working with segway — segway — probabilistic genome segmentation

SIRIUS routing skill for metabolomics and lipidomics LC-MS/MS compound identification. Use this skill when users mention SIRIUS, CSI:FingerID, CANOPUS, ZODIAC, molecular formula prediction, structure

Use when working with SNPRelate — a Bioconductor R package for high-performance SNP-based population genetics analysis. Supports principal component analysis (PCA), identity by descent (IBD), Fst esti

Subread — high-performance read alignment and quantification package using a seed-and-vote mapping strategy. Includes subread-align for genomic DNA and RNA-seq read alignment, subjunc for exon-junctio

tabix — fast random-access indexer for bgzip-compressed, tab-delimited genomic position files (VCF, BED, GFF3, GTF, SAM, and custom formats). Creates .tbi or .csi index files enabling sub-second regio

TADbit — Python toolkit for end-to-end Hi-C data analysis including read mapping, contact matrix construction, ICE normalization, TAD (Topologically Associating Domain) detection, and 3D chromatin str

Use when working with TaxonKit — a cross-platform NCBI taxonomy toolkit for querying lineages, converting names to TaxIds, reformatting taxonomy strings, filtering by rank, computing lowest common anc

UMI-tools — Python toolkit for processing Unique Molecular Identifiers (UMIs) in sequencing data. Provides end-to-end UMI workflows including extraction from FASTQ reads, cell barcode demultiplexing f

UnMICST (Universal Multiplexed Image Segmentation and Classification Tool) — deep-learning nuclear segmentation for multiplexed tissue imaging. Generates probability maps (background, nucleus interior

vcflib is a C++ library and suite of command-line tools for parsing, filtering, merging, annotating, and transforming VCF (Variant Call Format) files. Use when users need to filter variants by INFO/FO

Velvet — de Bruijn graph short-read genome assembler for Illumina, Solexa, and 454 sequencing data. Runs as a two-stage pipeline: velveth builds the hash table and de Bruijn graph, velvetg traverses t

WhatsHap -- read-based phasing (haplotype assembly) of genomic variants from sequencing reads. Phases diploid and polyploid genomes using long reads (PacBio, ONT) or short reads (Illumina). Key subcom

AICSImageIO — Python library for reading and writing multi-dimensional microscopy image data. Supports CZI (Zeiss), LIF (Leica), ND2 (Nikon), OME-TIFF, TIFF, and DV formats via a unified AICSImage int

AMBER (Assisted Model Building with Energy Refinement) — suite of molecular dynamics simulation programs for biomolecular systems. Provides force fields (ff14SB, ff19SB, GAFF2), system preparation (tl

antiSMASH (antibiotic & Secondary Metabolite Analysis SHell) — genome mining tool for identifying and annotating biosynthetic gene clusters (BGCs) in bacterial and fungal genomes. Detects NRPS, PKS, t

Use when working with AUCell — an R/Python tool for scoring gene set activity in single cells using the Area Under the Curve (AUC) metric. Computes per-cell activity scores for gene sets (regulons, pa

AutoDock Vina — fast open-source molecular docking engine for predicting protein-ligand binding poses and affinities. Uses gradient-optimization conformational search with Vina, Vinardo, or AutoDock4

BAGEL2 — Bayesian Analysis of Gene Essentiality v2 for identifying essential genes from CRISPR/Cas9 knockout screens. Calculates Bayes Factors from fold-change distributions using reference sets of co

Use when working with bigsnpr — an R package for analysis of massive

BioPython.PDB -- Python module for structural biology and macromolecular structure analysis. Parses PDB and mmCIF files, navigates the Structure-Model-Chain-Residue-Atom (SMCRA) hierarchy, computes at

BioRender — web-based platform for creating professional scientific figures, illustrations, and diagrams. Use for designing publication-quality figures for research papers, grants, posters, and presen

Boltz-1 — open-source deep learning model for predicting biomolecular 3D structures and interactions, approaching AlphaFold3-level accuracy. Supports protein, DNA, RNA, and small-molecule ligand struc

Bonito — open-source PyTorch research basecaller for Oxford Nanopore Technologies (ONT) long-read sequencing. Designed for basecaller training and model development, not production basecalling (use Do

Use when working with BrainGlobe Atlas API (bg-atlasapi / brainglobe-atlasapi) — a Python library for programmatic access to standardized brain atlases including the Allen Mouse Brain Atlas, Waxholm r

Use when working with brainrender — a Python library for 3D visualization of neuroscience data including brain atlases, neuron morphologies, cell distributions, and volumetric data. Part of the BrainG

BUGS/WinBUGS — Bayesian inference Using Gibbs Sampling for complex hierarchical models via MCMC. Model specification in the BUGS language with stochastic (~) and deterministic (<-) nodes, 30+ distribu

buttery-eel — streaming Guppy/Dorado basecaller wrapper for Oxford Nanopore SLOW5/BLOW5 format long-read sequencing data. Streams reads from SLOW5 or BLOW5 files directly through a running Guppy serve

Caduceus — bi-directional DNA foundation model built on the Mamba state-space architecture for genomic sequence modeling. Provides bi-directional long-range sequence understanding with reverse complem

Canopy — Bayesian phylogenetic reconstruction of tumor subclonal architecture from somatic SNVs and copy number alterations (CNAs). Uses MCMC sampling to infer cancer evolutionary trees, estimate subc

Cas-OFFinder — OpenCL-accelerated off-target site finder for CRISPR/Cas RNA-guided endonucleases. Searches whole genomes for potential off-target sites with configurable mismatch thresholds, DNA/RNA b

CCP4 — Collaborative Computational Project Number 4 software suite for macromolecular X-ray crystallography. Provides programs for data processing (AIMLESS, POINTLESS), molecular replacement (Phaser),