bwa

name	bwa
description	Burrows–Wheeler short-read alignment (BWA-MEM) to contigs/genomes. Use this skill when working with bwa: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/lh3/bwa. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["mapping","alignment","short-read"]
upstream	https://github.com/lh3/bwa
stage	mapping

BWA / BWA-MEM

Upstream: BWA / BWA-MEM

Citation

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009). https://doi.org/10.1093/bioinformatics/btp324

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv (2013). https://doi.org/10.48550/arXiv.1303.3997

See also docs/references.md.

Analytical thinking

Classic alternative to Bowtie2 for coverage mapping. Prefer bwa-mem2 on large cohorts when available; keep identical PE cleaned reads as used for assembly.

How to run

conda install -c bioconda bwa  # if packaged; else follow upstream

bwa index contigs.fa
bwa mem -t 16 contigs.fa clean_1.fq.gz clean_2.fq.gz \
  | samtools sort -@ 8 -o temp/map/${id}.bam
samtools index temp/map/${id}.bam

Key parameters

| bwa mem -t | threads | | | index | bwa index | Once per reference |

Decision notes

• Stage: mapping (short reads)
• Prefer bwa-mem2 for speed when compatible; keep BWA when Methods require BWA-MEM
• Indexes ≠ Bowtie2 / strobealign

Related skills

bwa-mem2 · bowtie2 · samtools · coverm · tool-selection · metagenomics-workflow