BI
Literature
bio-longread-alignment
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FreedomIntelligence/OpenClaw-Medical-SkillsView
Literature
BI
bio-read-alignment-bwa-alignment
Maintainer FreedomIntelligence · Last updated April 1, 2026
Align short reads to reference genome with BWA-MEM.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-alignment-bwa-alignment
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- bwa-mem2 index reference.fa.
- bwa-mem2 mem -t 8 reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam.
Source Doc
Excerpt From SKILL.md
Single-end reads
bwa-mem2 mem -t 8 reference.fa reads.fq.gz > aligned.sam
## Add read group information (required for GATK)
bwa-mem2 mem -t 8 \
-R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA\tLB:lib1' \
reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam
Pipe to samtools for sorted BAM output
bwa-mem2 mem -t 8
-R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA'
reference.fa reads_1.fq.gz reads_2.fq.gz |
samtools sort -@ 4 -o aligned.sorted.bam -
Use cases
- Use bio-read-alignment-bwa-alignment for manuscript drafting and submission workflows.
- Apply bio-read-alignment-bwa-alignment when polishing research communication outputs.
Not for
- Do not treat this catalog entry as a substitute for the full upstream workflow.
Upstream Related Skills
- read-qc/fastp-workflow - Preprocess reads before alignment
- alignment-files/alignment-sorting - Post-alignment processing
- alignment-files/duplicate-handling - Mark duplicates
- variant-calling/variant-calling - Call variants from BAM
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