Agent skill

seq-wrangler

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

View SKILL.md on GitHub Repository
Stars 2,009
Forks 275

Install this agent skill to your Project

npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/seq-wrangler

Metadata

Additional technical details for this skill

openclaw 
{
    "os": [
        "macos",
        "linux"
    ],
    "emoji": "\ud83e\udd96",
    "always": false,
    "install": [
        {
            "bins": [
                "samtools"
            ],
            "kind": "brew",
            "formula": "samtools"
        },
        {
            "bins": [
                "bwa"
            ],
            "kind": "brew",
            "formula": "bwa"
        }
    ],
    "homepage": "https://github.com/ClawBio/ClawBio",
    "requires": {
        "env": [],
        "bins": [
            "python3",
            "samtools"
        ],
        "config": [],
        "anyBins": [
            "bwa",
            "bowtie2",
            "minimap2"
        ]
    }
}

SKILL.md

🦖 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).

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