name: seq-wrangler description: Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines. version: 0.1.0 metadata: openclaw: requires: bins:

• python3
• samtools

anyBins:

• bwa
• bowtie2
• minimap2

env: [] config: [] always: false emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] install:

• kind: brew

formula: samtools bins: [samtools]

• kind: brew

formula: bwa bins: [bwa]

🦖 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).