bwa — Burrows-Wheeler Alignment tool. Short, low-divergent DNA sequences mapper against a large reference

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}}

Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads with [M]arking 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.gz}}

Map pair-end reads (sequences) to indexed genome using 32 [t]hreads with FASTA/Q [C]omments (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.gz}}