bwa

Quick Start

• Command: bwa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bwa
• Version: 0.7.19-r1273
• Reference: See references/help.md for detailed usage

When To Use This Tool

• Align low-divergence DNA sequencing reads to a reference genome.
• Use bwa index to build the reference index and bwa mem for modern short-read alignment.
• Good default for WGS, targeted DNA-seq, and many standard Illumina DNA workflows.
• If unsure which BWA algorithm to use, bwa mem is the normal starting point.

Common Patterns

# 1) Build the BWA index
bwa index reference.fa

# 2) Paired-end alignment with read group
bwa mem \
  -t 16 \
  -R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA' \
  reference.fa \
  sample_R1.fastq.gz sample_R2.fastq.gz \
  > sample.sam

# 3) Single-end alignment
bwa mem \
  -t 8 \
  reference.fa \
  sample.fastq.gz \
  > sample.sam

Recommended Workflow

1. Build the BWA index from the exact reference FASTA used for the project.
2. Align with bwa mem, usually with explicit -t and a correct read-group line.
3. Convert, sort, and index the SAM/BAM output with samtools.
4. Check mapping rate and duplicate behavior before variant calling or coverage analysis.

Guardrails

• bwa is a dispatcher; bwa --help is not the interface you want, while bwa, bwa mem, and bwa index are.
• bwa mem expects an indexed reference; forgetting bwa index is a common failure mode.
• Add an @RG line for any workflow that will later merge BAMs or call variants.
• The usual output is SAM to stdout; redirect it explicitly or pipe it into downstream tools.