lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) observed · 2026-08-28
Health v2 · maintenance only
66/100
- Activity 96
- Release rhythm 8
- Longevity 100
How is this computed?
round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10) — computed 2026-09-03. Adoption (stars, forks) is never an input.
- gap_med: n/a
- age_days: 5711
- days_rel: 529
- days_push: 26
- n_releases_24m: 1
Adoption not part of the score
1766 stars · 579 forks observed · 2026-08-28
What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded
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
cli-tool · maturity maintenance
search-engine cli developer-tools bioinformatics cpp cli sequence-alignment fm-index short-read-aligner ngs dna-mapping sam-output linux macos
1 source
- readme: https://github.com/lh3/bwa · fetched 2026-08-28 · 775da86791ca
Member repositories
| Repository | Role | Health v2 |
|---|---|---|
| lh3/bwa | main | 66 |
For agents
Data as of 2026-08-30T08:39:29.467469+00:00 · Report a problem