Command-line tool

bwa

brew/bwa

Checked 25 Oct 2026, 21:09 UTC · Listing refreshed from Homebrew, winget, npm, Scoop and cargo; npm packages checked against OSV.dev

Burrow-Wheeler Aligner for pairwise alignment of DNA

Website Source

At a glance

Type

Command-line tool

Install on

macOS, Linux

Last checked

25 Oct 2026, 21:09 UTC

Install it

macOS

brew install bwa

Linux

brew install bwa

Index the reference genome

bwa index path/to/reference.fa

Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space

bwa mem -t 32 path/to/reference.fa path/to/read_single_end.fq.gz | gzip > path/to/alignment_single_end.sam.gz

Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space

bwa mem -t 32 path/to/reference.fa path/to/read_pair_end_1.fq.gz path/to/read_pair_end_2.fq.gz | gzip > path/to/alignment_pair_end.sam.gz

Related command-line tools

• lastz
  Pairwise aligner for DNA sequences
• minimap2
  Versatile pairwise aligner for genomic and spliced nucleotide sequences
• fastga
  Pairwise whole genome aligner
• burrow
  Kafka Consumer Lag Checking
• rna-star
  RNA-seq aligner
• rammap
  Extensible and performant aligner and read mapper sysinternals
• diamond
  Accelerated BLAST compatible local sequence aligner
• bowtie2
  Fast and sensitive gapped read aligner

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