seq-wrangler
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
Best use case
seq-wrangler is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
Teams using seq-wrangler should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/seq-wrangler/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How seq-wrangler Compares
| Feature / Agent | seq-wrangler | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 🦖 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).
Related Skills
wes-clinical-report-es
Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.
wes-clinical-report-en
Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
variant-annotation
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
ukb-navigator
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
target-validation-scorer
Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
struct-predictor
Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.
soul2dna
Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping
scrna-orchestrator
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
scrna-embedding
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.
rnaseq-de
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
repro-enforcer
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.