bwa

Index the reference genome

$ bwa index [path/to/reference.fa]

$ bwa mem -t 32 [path/to/reference.fa] [path/to/read.fq.gz] | gzip > [path/to/alignment.sam.gz]

$ 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]

$ 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]

$ 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]

bwa command [options] [arguments]

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.

-t threads

Number of CPU threads

Mark shorter splits as secondary (Picard compatible)

Append FASTA/Q comment to output

Read group header line

Output file name

index

Build index from reference genome

Map reads using BWA-MEM algorithm

Align reads (older algorithm)

Generate SAM from aln output

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.

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.

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