albert-ying/.autolab/acquired_skills/bwa-mapping
.autolab/acquired_skills/bwa-mapping/SKILL.md
# BWA Mapping Skill ## When to Use Use when mapping paired-end or single-end sequencing reads to a reference genome. ## Standard Workflow 1. Index reference genome: `bwa index reference.fasta` 2. Map reads: `bwa mem -t <threads> reference.fasta R1.fastq.gz R2.fastq.gz > aligned.sam` 3. Convert to sorted BAM: `samtools sort -o aligned.sorted.bam aligned.sam` 4. Index BAM: `samtools index aligned.sorted.bam` ## Key Decisions - Use BWA-MEM for reads >70bp (standard for Illumina HiSeq) - Add read
$ install --global
skillsauthnpx skillsauth add albert-ying/autonomous-lab .autolab/acquired_skills/bwa-mappingInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.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
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