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bwa

Burrows-Wheeler Alignment tool. tldr-pages

On Linux

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Linux

from tldr-pages, CC BY 4.0

Burrows-Wheeler Alignment tool. Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome.

Index the reference genome

bwa index path/to/reference.faIdentify

Map single-end reads (sequences) to indexed genome using 32 threads 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.gzIdentify

Map pair-end reads (sequences) to the indexed genome using 32 threads 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.gzIdentify

Map pair-end reads (sequences) to the indexed genome using 32 threads with Marking shorter split hits as secondary for output SAM file compatibility in Picard software and compress the result

bwa mem -M -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.gzIdentify

Map pair-end reads (sequences) to indexed genome using 32 threads with FASTA/Q Comments (e.g. BC:Z:CGTAC) appending to a compressed result

bwa mem -C -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.gzIdentify