albert-ying/autonomous-lab/bwa-mapping
Claude Code and agent skill by albert-ying/autonomous-lab
Trust tier 3
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Install
npx vskill@latest install albert-ying/autonomous-lab/bwa-mappingSKILL.md
BWA Mapping Skill
When to Use
Use when mapping paired-end or single-end sequencing reads to a reference genome.
Standard Workflow
- Index reference genome:
bwa index reference.fasta - Map reads:
bwa mem -t <threads> reference.fasta R1.fastq.gz R2.fastq.gz > aligned.sam - Convert to sorted BAM:
samtools sort -o aligned.sorted.bam aligned.sam - Index BAM:
samtools index aligned.sorted.bam
Key Decisions
- Use BWA-MEM for reads >70bp (standard for Illumina HiSeq)
- Add read group info with -R flag for downstream variant calling
- Use appropriate thread count for available CPU cores
Security
- Security scanPassed, 90 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryChecking.autolab/acquired_skills/bwa-mapping/SKILL.md
Popularity
- 7-day trend score
- 5
Not refreshed yet.
Works with
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