bwa

Burrows-Wheeler Alignment tool. Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome. More information: https://github.com/lh3/bwa.

• Index the reference genome:

bwa index path/to/reference.fa

• 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.gz

• 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.gz

• 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.gz

• 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.gz