Agent skill

seq-wrangler

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

FreedomIntelligencegithub.com/FreedomIntelligenceGitHub ↗
claude-code
Install
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill seq-wrangler --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 1
SKILL.md size: 2 KB
Bundled scripts: none
Version: 0.1.0
Path: skills/seq-wrangler/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 2,909
Language: Python
Read our review of the source →

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the 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).

What's inside
Steps it walks through
  1. Core Capabilities
  2. Dependencies
  3. Example Queries
  4. Status
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About this skill
What does the seq-wrangler skill do?

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

How do I install it?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill seq-wrangler --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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