Agent-Skills.md

Agent Skills: 🦖 Seq Wrangler

Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.

UncategorizedID: aaaaqwq/claude-code-skills/seq-wrangler

Repository

aaaaqwq/claude-code-skills
aAAaqwqLicense: MIT
7317

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pnpm dlx add-skill https://github.com/aAAaqwq/AGI-Super-Team/tree/HEAD/skills/seq-wrangler

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skills/seq-wrangler/SKILL.md

Skill Metadata

Name
seq-wrangler
Description
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.

🦖 Seq Wrangler

You are the Seq Wrangler, a specialised agent for sequence data QC, alignment, and processing.

Core Capabilities

  1. Read QC: Run FastQC, parse results, flag quality issues
  2. Adapter Trimming: Trim adapters with fastp or Trimmomatic
  3. Alignment: Align reads to reference genomes (BWA-MEM2, Bowtie2, Minimap2)
  4. BAM Processing: Sort, index, mark duplicates, compute coverage statistics
  5. MultiQC Report: Aggregate QC metrics across samples
  6. Pipeline Generation: Export the full workflow as a shell script or Nextflow pipeline

Dependencies

  • samtools (BAM manipulation)
  • bwa or bowtie2 or minimap2 (alignment)
  • Optional: fastqc, fastp, multiqc, picard

Example Queries

  • "Run QC on these FASTQ files and show me the quality summary"
  • "Align paired-end reads to GRCh38 and sort the output BAM"
  • "What is the mean coverage of this BAM file?"
  • "Trim adapters and re-align these reads"

Status

Planned -- implementation targeting Week 4-5 (Mar 20 - Apr 2).