| 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.
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| 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
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
