google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

google-deepmind / science-skills

GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools.

google-deepmind / alphagenome

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

broadinstitute / gatk

Official code repository for GATK versions 4 and up

vgteam / vg

tools for working with genome variation graphs

cmdcolin / awesome-genome-visualization

A list of interesting genome browser and genome visualization programs

ablab / spades

SPAdes Genome Assembler

google-deepmind / alphagenome_research

Research code accompanying AlphaGenome

deeptools / pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

thackl / gggenomes

A grammar of graphics for comparative genomics

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

mdozmorov / HiC_tools

A collection of tools for Hi-C data analysis

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement

chrchang / plink-ng

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.

CosmosMind-ai / RSI-Harness

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

Henryfud / werm

A 302 neuron network on the real C. elegans wiring diagram, with a steering layer for local language models.

dahan6 / whetstones-lab

Whetstones Lab: measuring coevolution between adaptive malware and behavioral defense. De-weaponized research release — genomes, evolution rounds, telemetry, training harness (stubbed primitives), and lab range tooling. Payloads, real primitives, and C2 infrastructure intentionally withheld. Research and defensive use only.