# lh3/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Repository: https://github.com/lh3/bwa
Canonical: https://ross.abutalabs.com/products/bwa
Language: C
License: GPL-3.0
License Family: copyleft
Topics: bioinformatics, sequence-alignment, genomics, fm-index
Last push: 2026-08-07T13:43:25+00:00

## Health v2 (maintenance only)
Score: 66/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 96, release rhythm 8, longevity 100
- inputs: {"age_days": 5711, "days_push": 26, "days_rel": 529, "gap_med": null, "n_releases_24m": 1}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1766, forks 579 (observed 2026-08-28T04:05:33.484480+00:00)

## What it is
BWA (Burrow-Wheeler Aligner) is a command-line tool for mapping short DNA sequencing reads against large reference genomes such as the human genome. It builds an FM-index of the reference and offers three alignment algorithms, with BWA-MEM being the recommended one for most modern use cases.

## Use cases
- align illumina short reads to a reference genome
- map dna sequences against the human genome
- build an fm-index for a fasta reference
- produce sam/bam alignments from fastq files
- align paired-end sequencing reads
- find chimeric alignments for longer reads

## When to choose
- you need the standard, widely-cited short-read aligner for genomics pipelines
- you require exact legacy BWA-MEM output for reproducibility
- you are aligning Illumina reads up to a few hundred bp against a large genome

## When to avoid
- you are aligning long reads (use minimap2 instead)
- you need maximum speed for short reads (consider bwa-mem2 or minibwa)
- you want an actively developed tool with new features

## Facets
- artifact type: cli-tool
- maturity: maintenance
- function: search-engine, cli, developer-tools
- domain: bioinformatics
- platform: cpp, cli
- tags: sequence-alignment, fm-index, short-read-aligner, ngs, dna-mapping, sam-output, linux, macos

## Member repositories
- lh3/bwa (main) score 66

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:05:33.484480+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T03:26:29.764727+00:00, confidence not recorded.
  - readme: https://github.com/lh3/bwa (fetched 2026-08-28T04:05:33.484480+00:00, sha 775da86791ca)
- Data as of 2026-08-30T08:39:29.467469+00:00.