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seq-wrangler

Maintainer FreedomIntelligence · Last updated April 1, 2026

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

OpenClawNanoClawAnalysisReproductionseq-wrangler⚙️ clawbio pipelinesbioinformatics orchestration & pipelinessequence

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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

Source Doc

Excerpt From SKILL.md

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).

Use cases

  • Use seq-wrangler for genomics and bioinformatics workflows.
  • Apply seq-wrangler to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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