DeepVariant
github.com/google/deepvariantDeep learning-based variant caller
Sourced from
- Awesome Bioinformatics — github.com/google/deepvariant
- Awesome AI for Science — github.com/google/deepvariant
- GitHub — github.com/google/deepvariant
Related resources
Foundation models for genomics and transcriptomics pretrained on 3,000+ human genomes and 850+ diverse species, enabling chromatin accessibility prediction, splice site detection, and promoter classification across multiple model scales (InstaDeep, NVIDIA & TUM, Nature Methods 2023)
Deep-learning germline small-variant caller for long-read sequencing (PacBio HiFi/ONT) combining fast pileup calling with haplotype-resolved full-alignment calling; widely adopted as a standard in the Human Pangenome Reference Consortium production pipelines and PrecisionFDA truth challenges, with pre-trained models for multiple sequencing platforms, bioconda/Docker distribution, and a companion Clair-skills agent plugin for Claude Code/Codex (HKU-BAL, 394+ stars, BSD-3-Clause, actively maintained)
MCP server enabling spatial transcriptomics analysis via natural language, integrating 60+ methods including SpaGCN, Cell2location, LIANA+, CellRank for Visium, Xenium, MERFISH platforms
Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.
Therapeutics Data Commons: 66 AI-ready datasets across 22 drug discovery tasks with 29 leaderboards, covering target identification, molecular generation, ADMET prediction, and clinical trial outcomes (Harvard MIMS, NeurIPS 2021/2024)