Genomic Pipelines Skills
Seven bioinformatics skills for Claude Code: variant calling, RNA-seq, QC, and annotation pipelines.
About
A compact collection of seven bioinformatics skills for Claude Code covering the core genomic analysis loop: WGS/WES variant calling (GATK, DeepVariant, Mutect2), bulk and single-cell RNA-seq (DESeq2, Seurat, Scanpy), ChIP/ATAC-seq, variant annotation (VEP, SnpEff, ANNOVAR), QC and preprocessing (FastQC, MultiQC), and CNV/SV detection. Each skill ships command-line examples, tool comparison tables, nf-core pipeline recommendations, and quality thresholds aligned with GATK and ENCODE best practices. MIT licensed, prompt-based with no extra dependencies beyond the Claude Code CLI.
Caveats: this is a small community repo (3 stars, 2 commits), so treat it as a curated cheat-sheet rather than a maintained platform. The README's install snippet still contains a your-username placeholder, a sign of light maintenance; the copy-the-.claude-folder path is the reliable one.
What it can do
- WGS/WES variant calling guidance
- RNA-seq analysis (bulk and single-cell)
- ChIP/ATAC-seq peak calling workflows
- Variant annotation with VEP and SnpEff
- QC pipelines with FastQC and MultiQC
- CNV and structural variant detection
Setup
Clone the repo with git clone https://github.com/maratgaliev/claude-skill-genomic-pipelines.git and copy the .claude folder into your project (cp -r claude-skill-genomic-pipelines/.claude /path/to/your/project/). Invoke with /genomics, /genomics:wgs, /genomics:rnaseq, or /genomics:cnv.
Prerequisites
Claude Code CLI; the underlying bioinformatics tools (GATK, samtools, etc.) installed separately for any commands you actually run.
Use cases
Works with
Trust score — 6/10
Scored 6/10 (metrics tier, metrics-v1). Evidence: 3 GitHub stars, MIT license, 7 bioinformatics skills; Covers GATK, DeepVariant, DESeq2, Seurat, VEP per GATK/ENCODE best practices; Caveat: tiny repo (2 commits), README install snippet has your-username placeholder; treat as curated reference.
★ 3 GitHub stars
Sources
Every fact above was checked against these sources. Where a claim comes from the provider and couldn't be independently verified, the text says so.