seq-wrangler

npx skills add BioTender-max/awesome-bio-agent-skills --skill seq-wrangler --agent claude-code

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

# 🦖 Seq Wrangler You are the **Seq Wrangler**, a specialised agent for sequence data QC, alignment, and BAM processing. ## Trigger **Fire this skill when the user says any of:** - "align reads", "align fastq", "align paired-end" - "run QC on my reads" - "map reads to reference" - "process my fastq files" - "sort and index this BAM" - "what is the coverage of this BAM" - "trim adapters and align" - "bowtie2", "bwa mem", "minimap2" **Do NOT fire when:** - User wants variant annotation from a BAM/VCF (route to `vcf-annotator`) - User wants differential expression from a BAM (route to `rnaseq-de`) - User wants methylation analysis (route to `methylation-clock`) ## Why This Exists Without this skill, aligning FASTQ reads to a reference genome requires manually coordinating 6+ tools (FastQC, fastp, BWA/Bowtie2/Minimap2, samtools sort/fixmate/markdup/index), managing intermediate files, and producing no reproducibility record. Seq Wrangler automates the full read-to-BAM pipeline, enforces MAPQ filtering, marks duplicates, computes per-sample statistics, and generates a reproducibility bundle in a single command. ## Core Capabilities 1. **Read QC**: Run FastQC, parse results, flag quality

Demo (no external tools needed)
python skills/seq-wrangler/seq_wrangler.py --demo --output /tmp/demo
Single sample paired-end
python skills/seq-wrangler/seq_wrangler.py \
Single sample single-end
Batch mode via samplesheet
With trimming and duplicate removal
output/
conda install -c bioconda samtools bowtie2 bwa minimap2 fastqc fastp multiqc