bio-read-alignment-bwa-alignment - Align DNA short reads with BWA-MEM2
Align paired-end or single-end DNA short reads to a reference genome with BWA-MEM2 or BWA-MEM, including read groups and BAM output preparation.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Align paired-end reads
- Align single-end reads
- Build reference indexes
- Inject read groups
- Stream coordinate-sorted BAM
- Prepare duplicate-marked BAM
- Preserve SV split reads
- Support ALT-aware mapping
Inputs
- DNA FASTQ reads
- Reference genome FASTA
- Read-group metadata
- Reference ALT/decoy files
- Output BAM path
Outputs
- Aligned BAM file
- Coordinate-sorted BAM file
- Duplicate-marked BAM file
- BAM index file
- Alignment records with read groups
- Supplementary split alignments
Requirements
- bwa-mem2 2.2.1 or later
- BWA 0.7.17 or later
- samtools 1.19 or later
- Command-line execution environment
- Sufficient compute and memory
- ALT-aware downstream support for ALT mapping