#genomics

Embeddable genomic visualization component based on the Integrative Genomics Viewer

JAMMA (Highly-Accelerated Multi-method Mixed-model Association) -- a fast and modern Python and C reimplementation of GEMMA for large-scale GWAS.

MGnify Assembly Analysis Pipeline

Parser for bigwig and bigbed files

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Monorepo for Apollo 3 server-side and client-side (JBrowse 2 plugin) components.

cython + htslib == fast VCF and BCF processing

The self-evolving agentic framework for bioinformatics

An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

A high efficiency binary format for sequencing data

MCP interface to BioPython