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bwa

Map DNA sequences against a reference genome

TLDR

Index the reference genome
$ bwa index [path/to/reference.fa]
Map single-end reads to indexed genome
$ bwa mem -t 32 [path/to/reference.fa] [path/to/read.fq.gz] | gzip > [path/to/alignment.sam.gz]
Map pair-end reads to indexed genome
$ bwa mem -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]
Map with Picard compatibility (mark shorter splits as secondary)
$ bwa mem -M -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]
Map with FASTA/Q comments appended
$ bwa mem -C -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]

SYNOPSIS

bwa command [options] [arguments]

DESCRIPTION

bwa (Burrows-Wheeler Aligner) is a software package for mapping low-divergent DNA sequences against a large reference genome, such as the human genome. It uses the Burrows-Wheeler Transform to build an index of the reference.The mem algorithm is recommended for most applications, supporting reads from 70bp to a few megabases and providing accurate mapping.

PARAMETERS

-t threads

Number of CPU threads
-M
Mark shorter splits as secondary (Picard compatible)
-C
Append FASTA/Q comment to output
-R string
Read group header line
-o file
Output file name

SUBCOMMANDS

index

Build index from reference genome
mem
Map reads using BWA-MEM algorithm
aln
Align reads (older algorithm)
samse/sampe
Generate SAM from aln output

INSTALL

sudo apt install bwa
sudo dnf install bwa
brew install bwa
nix profile install nixpkgs#bwa

CAVEATS

Indexing large genomes requires significant memory and time. Output is uncompressed SAM by default; pipe through gzip for storage. Quality of results depends on read quality and reference completeness.

HISTORY

BWA was developed by Heng Li and first published in 2009. The MEM algorithm was introduced in 2013 and has become the preferred method for most mapping tasks.

SEE ALSO

samtools(1), bowtie2(1), minimap2(1)

RESOURCES

Source code · Homepage