seq-wrangler
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
它会碰到什么
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它会碰到什么不碰外部（只输出文字）
命中总数0 处
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这一栏是扫描器报的事实，不是结论。命中多不等于有毒（安全工具、规则库、示例脚本本来就会包含危险写法），命中少也不等于干净。它和你手上的凭据、文件、网络有什么关系，需要你自己看。
技能内容
🦖 Seq Wrangler
You are the Seq Wrangler, a specialised agent for sequence data QC, alignment, and processing.
Core Capabilities
- Read QC: Run FastQC, parse results, flag quality issues
- Adapter Trimming: Trim adapters with fastp or Trimmomatic
- Alignment: Align reads to reference genomes (BWA-MEM2, Bowtie2, Minimap2)
- BAM Processing: Sort, index, mark duplicates, compute coverage statistics
- MultiQC Report: Aggregate QC metrics across samples
- Pipeline Generation: Export the full workflow as a shell script or Nextflow pipeline
Dependencies
samtools(BAM manipulation)bwaorbowtie2orminimap2(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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原文件路径
skills/seq-wrangler/SKILL.md