freebayes

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  "build_dependencies": [
    "cmake",
    "meson",
    "ninja",
    "pkgconf",
    "simde",
    "wfa2-lib"
  ],
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  "dependencies": [
    "htslib",
    "tabixpp"
  ],
  "deprecated": 0,
  "deprecation_reason": null,
  "desc": "Bayesian haplotype-based genetic polymorphism discovery and genotyping",
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  "enrichment_fetched_at": "2026-06-20T23:37:48+00:00",
  "first_seen": "2026-06-20T23:34:18+00:00",
  "full_name": "freebayes",
  "github_default_branch": "master",
  "github_last_commit_at": "2026-04-20T19:20:01Z",
  "github_readme_excerpt": "# *freebayes*, a haplotype-based variant detector\n## user manual and guide\n\n\n[![Github-CI](https://github.com/freebayes/freebayes/workflows/CI/badge.svg)](https://github.com/freebayes/freebayes/actions) [![DL](https://anaconda.org/bioconda/freebayes/badges/downloads.svg)](https://anaconda.org/bioconda/freebayes) [![BrewBadge](https://img.shields.io/badge/%F0%9F%8D%BAbrew-freebayes-brightgreen.svg)](https://github.com/brewsci/homebrew-bio) [![Guix](https://packages.guix.gnu.org/packages/freebayes/badges/latest-version.svg)](https://packages.guix.gnu.org/packages/freebayes) [![DebianBadge](https://badges.debian.net/badges/debian/testing/freebayes/version.svg)](https://tracker.debian.org/pkg/freebayes) [![Chat on Matrix](https://matrix.to/img/matrix-badge.svg)](https://matrix.to/#/#vcflib:matrix.org)\n--------\n\nNote that CI tests may fail until vcflib is updated on the main distros to 1.0.13. This is because of the location of vcflib include files moved to /usr/include/vcflib.\n\n## Overview\n\n[*freebayes*](http://arxiv.org/abs/1207.3907) is a\n[Bayesian](http://en.wikipedia.org/wiki/Bayesian_inference) genetic variant\ndetector designed to find small polymorphisms, specifically SNPs\n(single-nucleotide polymorphisms), indels (insertions and deletions), MNPs\n(multi-nucleotide polymorphisms), and complex events (composite insertion and\nsubstitution events) smaller than the length of a short-read sequencing\nalignment.\n\n*freebayes* is haplotype-based, in the sense that it calls variants based on\nthe literal sequences of reads aligned to a particular target, not their\nprecise alignment.  This model is a straightforward generalization of previous\nones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on\nalignments.  This method avoids one of the core problems with alignment-based\nvariant detection--- that identical sequences may have multiple possible\nalignments:\n\n\u003cimg src=\"https://github.com/freebayes/freebayes/raw/v1.3.0/paper/haplotype_calling.png\" width=50",
  "github_repo": "freebayes/freebayes",
  "github_stars": 871,
  "github_topics": [],
  "homepage": "https://github.com/freebayes/freebayes",
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  "homepage_og_image": null,
  "homepage_title": null,
  "installs_30d": 4,
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  "installs_90d": 21,
  "keg_only": 0,
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  "last_seen": "2026-06-20T23:34:18+00:00",
  "license": "MIT",
  "llm_generated_at": null,
  "llm_model": null,
  "name": "freebayes",
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  "one_liner": null,
  "optional_dependencies": [],
  "rank_30d": 11618,
  "rank_365d": 8684,
  "rank_90d": 9550,
  "raw_hash": "6c89fb92f0462f8d",
  "recommended_dependencies": [],
  "revision": 0,
  "ruby_source_path": "Formula/f/freebayes.rb",
  "tap": "homebrew/core",
  "test_dependencies": [],
  "uses_from_macos": [],
  "version_head": "HEAD",
  "version_stable": "1.3.10",
  "versioned_formulae": [],
  "why_use_this": null
}