name: bwa description: > Burrows–Wheeler short-read alignment (BWA-MEM) to contigs/genomes. Use for installation, parameter choice, execution, output interpretation, or troubleshooting. license: MIT metadata: version: "1.0.1" metagenomics.category: "analysis-tools" metagenomics.tags: "mapping, alignment, short-read" metagenomics.upstream: "https://github.com/lh3/bwa" metagenomics.stage: "mapping" metagenomics.maturity: "reviewed-legacy" metagenomics.last-reviewed: "2026-10-24" metagenomics.command-status: "BWA-MEM/Samtools paired-end template statically reviewed; not executed here"

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

Build an index with an explicit prefix and retain the exact reference checksum.

set -Eeuo pipefail
id="${1:?usage: map-one.sh SAMPLE_ID REF R1 R2 OUTPUT_DIR}"
ref="${2:?usage: map-one.sh SAMPLE_ID REF R1 R2 OUTPUT_DIR}"
r1="${3:?usage: map-one.sh SAMPLE_ID REF R1 R2 OUTPUT_DIR}"
r2="${4:?usage: map-one.sh SAMPLE_ID REF R1 R2 OUTPUT_DIR}"
out="${5:?usage: map-one.sh SAMPLE_ID REF R1 R2 OUTPUT_DIR}"
threads="${THREADS:-16}"
[[ "$id" =~ ^[A-Za-z0-9][A-Za-z0-9._-]*$ ]] || exit 2
for input in "$ref" "$r1" "$r2"; do test -s "$input" || exit 2; done
test ! -e "$out" || { echo "use a new output directory: $out" >&2; exit 2; }
mkdir -p "$out/index"
 
bwa index -p "$out/index/reference" "$ref" \
  >"$out/bwa-index.stdout.log" 2>"$out/bwa-index.stderr.log"
bwa mem -t "$threads" "$out/index/reference" "$r1" "$r2" \
  2>"$out/${id}.bwa.stderr.log" \
  | samtools sort -@ "$threads" -o "$out/${id}.bam" -
samtools index "$out/${id}.bam"

Key parameters

Decision notes

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

Validation, recovery, and provenance

samtools quickcheck -v "$out/${id}.bam"
samtools view -H "$out/${id}.bam" | grep -q '^@HD.*SO:coordinate'
test -s "$out/${id}.bam.bai"
samtools flagstat -@ 4 -O tsv "$out/${id}.bam" >"$out/${id}.flagstat.tsv"

Inspect paired/primary mapping rates, insert-size behavior, reference contig names, and depth distribution before coverage or binning. Failed streams can leave partial BAMs, so publish/rename only after validation. Record BWA and Samtools versions, reference/read checksums, read-group policy, full command, logs, flagstat, and BAM checksum.

Related skills

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