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JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Python library to facilitate genome assembly, annotation, and comparative genomics

Official home of genome aligner based upon notion of Cactus graphs

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive update to it.

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

UCSC Genome Browser source. "beta" is released version / "master" is testing.

Eukaryotic Genome Annotation Pipeline

Fast, flexible and extensible genome browser.

SPAdes Genome Assembler

Fast Whole-Genome Similarity (ANI) Estimation

python module to plot beautiful and highly customizable genome browser tracks

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A visualization grammar and GPU-accelerated toolkit for genomic data

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

A genome visualization python package for comparative genomics

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

Genome modeling and design across all domains of life

Genome viewer for you and your agents.

A deterministic genomics engine with a compact memory footprint. Run whole-genome workloads in as little as 100 MB RAM. Built in Rust.

Empryo issue tracker + SoulForge (v2) archive — Empryo is the graph-powered AI coding agent that edits symbols, not strings: AST surgery, full LSP, a live code genome. Get it at https://empryo.com

Machine Genome is an open identity and provenance protocol for models, agents, harnesses, datasets, and the artifacts that connect them.

RSIH — versionable, shareable agent harness: Pi coding agent + Genome config layer