SyntaxStandard

bwa

Verified for current stable LTS

Bwa Commands

Bwa command syntax with verified terminal examples.

Commands

5 commands for Bwa

bwa

Bwa Command: Index Reference Genome Linux

bwa index <path/to/reference.fa>
bwa

Bwa Command: Map Pair End Reads Append Comments Linux

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>
bwa

Bwa Command: Map Pair End Reads Linux

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>
bwa

Bwa Command: Map Pair End Reads Mark Secondary Linux

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>
bwa

Bwa Command: Map Single End Reads Linux

bwa mem -t 32 <path/to/reference.fa> <path/to/read_single_end.fq.gz> | gzip > <path/to/alignment_single_end.sam.gz>

Suggest a Bwa Command

Submit missing workflows, corrections, or verified alternatives for this tool.

FAQ

Coverage: Focused examples for common Bwa workflows.

Verified version: current stable LTS.

Verification: Test commands in a disposable workspace and submit notes for edge cases.