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bioinformatics-engineering

v0.1.2

Bioinformatics & genomics-pipeline team — agents (bioinformatics-workflow-architect, genomics-pipeline-engineer) for the layer answering 'which workflow engine, reference, and compute strategy, and how do we build a reproducible, validated genomics pipeline?': engine choice (Nextflow/nf-core, Snakemake, WDL+Cromwell/miniwdl, CWL), reference build (GRCh38 vs T2T-CHM13) + core steps (QC, trimming, alignment BWA-MEM2/minimap2/STAR/Salmon, dedup, variant calling GATK/DeepVariant, joint genotyping), RNA-seq (DESeq2/edgeR) and single-cell (Scanpy/Seurat), reproducibility (Docker/Apptainer, Conda/Bioconda, pinned versions, FAIR, provenance), HPC-vs-cloud scaling and cost, and validation vs GIAB/hap.py truth sets. skills, a knowledge bank (pipeline decision tree + 2026 workflow-patterns reference), and templates. Distinct from ml-engineering (generic MLOps/model training), clinical-trials (trial operations/regulatory), and data-platform (warehouse/BI). Requires ravenclaude-core@>=0.7.0.

Claude Code3 Skills

By Matt CorbettLicense: MIT7 GitHub starsUpdated last week

Directory evidence

Runtimes
Claude Code
Parsed components
3 skill or MCP entries
Source updated
Sep 15, 2026
Manifest status
Canonical path parsed

The directory validates manifest shape and source location. It does not execute the plugin or provide a security endorsement. Review the indexing methodology →

Install bioinformatics-engineering for Claude Code

Installs for the current user
claude plugin marketplace add IchenDEV/agent-plugin-mkt
claude plugin marketplace update agent-plugin-marketplace
claude plugin install bioinformatics-engineering@agent-plugin-marketplace

Paste and run these commands in a terminal with Claude Code. They add and refresh the PluginsMP catalog, then install this plugin.

The installer fetches third-party code from the source repository shown on this page. This directory validates manifest structure and source location, but does not perform a security audit; review the manifest, components, and source before installing.

Get the source manually
git clone https://github.com/mcorbett51090/RavenClaude

Clone the source repository, then follow its setup instructions to add the plugin to a compatible client. The plugin root is plugins/bioinformatics-engineering/.

Plugin files

plugins/bioinformatics-engineering/
├── .claude-plugin/plugin.json
├── skills/choose-bioinformatics-pipeline-and-stack/SKILL.md
├── skills/design-genomics-analysis-workflow/SKILL.md
└── skills/implement-and-scale-bioinformatics-pipeline/SKILL.md

Included Skills3

choose-bioinformatics-pipeline-and-stackskills/choose-bioinformatics-pipeline-and-stack/SKILL.md

Pick the right genomics workflow engine, reference build, tool chain, compute strategy, and reproducibility approach for a described analysis by traversing the bioinformatics pipeline decision tree (assay/question → curated community pipeline exists? → portability/team fluency → HPC vs cloud → reference build), then return the recommended engine (Nextflow/nf-core / Snakemake / WDL+Cromwell / CWL), the reference (GRCh38 vs T2T-CHM13) with the build hazards, the aligner/variant-caller chain, the compute plan (Slurm vs cloud Batch/spot + cost shape), the reproducibility approach, the validation truth set, and the conditions that would flip the choice. Reach for this when the user asks "Nextflow vs Snakemake vs WDL?", "GRCh38 or T2T-CHM13?", "HPC or cloud for this pipeline?", or "how do we make this reproducible?". Used by `bioinformatics-workflow-architect` (primary).

design-genomics-analysis-workflowskills/design-genomics-analysis-workflow/SKILL.md

From a scientific question, an assay, and a sample design, derive the concrete genomics analysis workflow — the per-sample step graph (QC, trimming, alignment, dedup, BQSR-or-not, variant calling or quantification), the cohort/joint step (joint genotyping or differential-expression model), the reference build and its matching accessory files, and the validation truth set — captured as an analysis plan. Reach for this when the user asks "design the WGS germline workflow", "what steps does this RNA-seq analysis need?", or "how do we structure the per-sample and cohort steps?". Used by `genomics-pipeline-engineer` and `bioinformatics-workflow-architect`.

implement-and-scale-bioinformatics-pipelineskills/implement-and-scale-bioinformatics-pipeline/SKILL.md

Implement a designed genomics workflow in the chosen engine, containerize and pin every tool for reproducibility, scale it with scatter/gather on HPC Slurm or cloud Batch (spot on the fault-tolerant steps), and validate it against a GIAB/GA4GH hap.py truth set — then produce a pipeline-validation report. Reach for this when the user asks "build this pipeline in Nextflow/Snakemake/WDL", "containerize and pin it for reproducibility", "scale/cost-optimize this on Slurm or cloud", or "benchmark our variant calls against GIAB". Used by `genomics-pipeline-engineer` (primary).

Plugin manifests1

plugins/bioinformatics-engineering/.claude-plugin/plugin.json
{
  "name": "bioinformatics-engineering",
  "version": "0.1.2",
  "description": "Bioinformatics & genomics-pipeline team — agents (bioinformatics-workflow-architect, genomics-pipeline-engineer) for the layer answering 'which workflow engine, reference, and compute strategy, and how do we build a reproducible, validated genomics pipeline?': engine choice (Nextflow/nf-core, Snakemake, WDL+Cromwell/miniwdl, CWL), reference build (GRCh38 vs T2T-CHM13) + core steps (QC, trimming, alignment BWA-MEM2/minimap2/STAR/Salmon, dedup, variant calling GATK/DeepVariant, joint genotyping), RNA-seq (DESeq2/edgeR) and single-cell (Scanpy/Seurat), reproducibility (Docker/Apptainer, Conda/Bioconda, pinned versions, FAIR, provenance), HPC-vs-cloud scaling and cost, and validation vs GIAB/hap.py truth sets. skills, a knowledge bank (pipeline decision tree + 2026 workflow-patterns reference), and templates. Distinct from ml-engineering (generic MLOps/model training), clinical-trials (trial operations/regulatory), and data-platform (warehouse/BI). Requires ravenclaude-core@>=0.7.0.",
  "author": {
    "name": "Matt Corbett"
  },
  "homepage": "https://github.com/mcorbett51090/RavenClaude",
  "license": "MIT",
  "keywords": [
    "bioinformatics",
    "genomics",
    "nextflow",
    "nf-core",
    "snakemake",
    "wdl",
    "variant-calling",
    "gatk",
    "rna-seq",
    "reference-genome",
    "reproducibility",
    "ngs-pipeline"
  ],
  "requires": {
    "plugins": [
      "ravenclaude-core@>=0.7.0"
    ]
  }
}

For maintainers

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[bioinformatics-engineering on Agent Plugins Marketplace](https://pluginsmp.com/plugins/bioinformatics-engineering)