bwa

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  "desc": "Burrow-Wheeler Aligner for pairwise alignment of DNA",
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  "enrichment_fetched_at": "2026-06-20T23:36:03+00:00",
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  "full_name": "bwa",
  "github_default_branch": "master",
  "github_last_commit_at": "2026-06-20T14:43:47Z",
  "github_readme_excerpt": "[![Build Status](https://github.com/lh3/bwa/actions/workflows/ci.yaml/badge.svg)](https://github.com/lh3/bwa/actions)\n[![SourceForge Downloads](https://img.shields.io/sourceforge/dt/bio-bwa.svg?label=SF%20downloads)](https://sourceforge.net/projects/bio-bwa/files/?source=navbar)\n[![GitHub Downloads](https://img.shields.io/github/downloads/lh3/bwa/total.svg?style=flat\u0026label=GitHub%20downloads)](https://github.com/lh3/bwa/releases)\n[![BioConda Install](https://img.shields.io/conda/dn/bioconda/bwa.svg?style=flag\u0026label=BioConda%20install)](https://anaconda.org/bioconda/bwa)\n\n\u003e [!Note]\n\u003e BWA-MEM has been replaced by [minimap2][minimap2] for long reads\n\u003e and will be replaced by [minibwa][minibwa] for short reads.\n\u003e If you still prefer the exact legacy output of BWA-MEM, give [BWA-MEM2][bwa-mem2] a try.\n\u003e The original bwa-aln algorithm is still unique due to its sensitivity to very short reads.\n\n[minimap2]: https://github.com/lh3/minimap2\n[bwa-mem2]: https://github.com/bwa-mem2/bwa-mem2\n[minibwa]: https://github.com/lh3/minibwa\n\n## Getting started\n\n\tgit clone https://github.com/lh3/bwa.git\n\tcd bwa; make\n\t./bwa index ref.fa\n\t./bwa mem ref.fa read-se.fq.gz | gzip -3 \u003e aln-se.sam.gz\n\t./bwa mem ref.fa read1.fq read2.fq | gzip -3 \u003e aln-pe.sam.gz\n\n## Introduction\n\nBWA is a software package for mapping DNA sequences against a large reference\ngenome, such as the human genome. It consists of three algorithms:\nBWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina\nsequence reads up to 100bp, while the rest two for longer sequences ranged from\n70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the\nsupport of long reads and chimeric alignment, but BWA-MEM, which is the latest,\nis generally recommended as it is faster and more accurate. BWA-MEM also has\nbetter performance than BWA-backtrack for 70-100bp Illumina reads.\n\nFor all the algorithms, BWA first needs to construct the FM-index for the\nreference genome (the **index** command). Ali",
  "github_repo": "lh3/bwa",
  "github_stars": 1752,
  "github_topics": [
    "bioinformatics",
    "fm-index",
    "genomics",
    "sequence-alignment"
  ],
  "homepage": "https://github.com/lh3/bwa",
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  "last_seen": "2026-06-20T23:34:18+00:00",
  "license": "GPL-3.0-or-later AND MIT",
  "llm_generated_at": null,
  "llm_model": null,
  "name": "bwa",
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  "ruby_source_path": "Formula/b/bwa.rb",
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  "version_head": "HEAD",
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