Skillshub seq-wrangler

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

install

source · Clone the upstream repo

git clone https://github.com/ComeOnOliver/skillshub

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/ComeOnOliver/skillshub "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/ClawBio/ClawBio/seq-wrangler" ~/.claude/skills/comeonoliver-skillshub-seq-wrangler && rm -rf "$T"

manifest: skills/ClawBio/ClawBio/seq-wrangler/SKILL.md

source content

🦖 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)
```
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).