---
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: [darwin, 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).



---
Source attribution: ClawBio
Original project: https://github.com/ClawBio/ClawBio
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 SkillsHub Contributors

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: ClawBio
Original project: https://github.com/ClawBio/ClawBio
Attribution basis: Explicit original project field in package

Fields of work: Data & Analytics, Education & Research
Roles: Business Intelligence Analyst, Data Scientist, Researcher
Specialties: API
Tools: Bowtie2, Bwa, Fastp, Fastqc, Multiqc, Picard, Samtools, Trimmomatic
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 1b8652ee7649397f2d616bfddd98d43bea8bb094791261fbf6ad571387a61530
Metadata reviewed: 2026-10-27
This metadata supersedes earlier Mega AI Hub catalog attribution. Original instruction and supporting files are preserved.