bioinformatics

name	bioinformatics
description	Use when the user asks about bioinformatics, genomics, sequencing, variant calling, gene expression, single-cell analysis, protein structure, pharmacogenomics, metagenomics, phylogenetics, computational biology, RNA-seq, ChIP-seq, ATAC-seq, epigenomics, CRISPR, proteomics, population genetics, GWAS, genome assembly, structural biology, chemoinformatics, pathway analysis, immunoinformatics, metabolomics, systems biology, or any computational biology task. Gateway to 400+ genomics and computational biology skills from bioSkills and ClawBio open-source libraries.
license	MIT
metadata	{"author":"Hermes Agent (MIT)","version":"1.0.0","source":"https://github.com/NousResearch/hermes-agent/tree/main/optional-skills/research/bioinformatics"}
allowed-tools	read_file, write_file, patch, search_files, system_exec, python_interpreter, load_markdown_skill, delegate_task, vision

Bioinformatics Skills Gateway

Use when asked about bioinformatics, genomics, sequencing, variant calling, gene expression, single-cell analysis, protein structure, pharmacogenomics, metagenomics, phylogenetics, or any computational biology task.

This skill is a gateway to two open-source bioinformatics skill libraries. Instead of bundling hundreds of domain-specific skills, it indexes them and fetches what you need on demand.

The git clone / cat / pip / conda / apt / brew / Rscript commands below run via the system_exec tool. Cloned repos are fetched on demand and never committed to the workspace.

Sandbox note: the git clone commands need outbound network access. Under hakase's bubblewrap sandbox mode, set allow_network: true in config.json under the sandbox block. Python packages installed via pip in the .venv also need allow_pip_install: true.

Sources

• bioSkills -- 385 reference skills (code patterns, parameter guides, decision trees) Repo: https://github.com/GPTomics/bioSkills Format: SKILL.md per topic with code examples. Python/R/CLI.

• ClawBio -- 33 runnable pipeline skills (executable scripts, reproducibility bundles) Repo: https://github.com/ClawBio/ClawBio Format: Python scripts with demos. Each analysis exports report.md + commands.sh + environment.yml.

How to fetch and use a skill

1. Identify the domain and skill name from the index below.
2. Clone the relevant repo (shallow clone to save time):

   # bioSkills (reference material)
   git clone --depth 1 https://github.com/GPTomics/bioSkills.git /tmp/bioSkills
   
   # ClawBio (runnable pipelines)
   git clone --depth 1 https://github.com/ClawBio/ClawBio.git /tmp/ClawBio
   

3. Read the specific skill:

   # bioSkills -- each skill is at: <category>/<skill-name>/SKILL.md
   cat /tmp/bioSkills/variant-calling/gatk-variant-calling/SKILL.md
   
   # ClawBio -- each skill is at: skills/<skill-name>/
   cat /tmp/ClawBio/skills/pharmgx-reporter/README.md
   

4. Follow the fetched skill as reference material. These are NOT Hermes-format skills -- treat them as expert domain guides. They contain correct parameters, proper tool flags, and validated pipelines.

Skill Index by Domain

Sequence Fundamentals

bioSkills: sequence-io/ -- read-sequences, write-sequences, format-conversion, batch-processing, compressed-files, fastq-quality, filter-sequences, paired-end-fastq, sequence-statistics sequence-manipulation/ -- seq-objects, reverse-complement, transcription-translation, motif-search, codon-usage, sequence-properties, sequence-slicing ClawBio: seq-wrangler -- Sequence QC, alignment, and BAM processing (wraps FastQC, BWA, SAMtools)

Read QC & Alignment

bioSkills: read-qc/ -- quality-reports, fastp-workflow, adapter-trimming, quality-filtering, umi-processing, contamination-screening, rnaseq-qc read-alignment/ -- bwa-alignment, star-alignment, hisat2-alignment, bowtie2-alignment alignment-files/ -- sam-bam-basics, alignment-sorting, alignment-filtering, bam-statistics, duplicate-handling, pileup-generation

Variant Calling & Annotation

bioSkills: variant-calling/ -- gatk-variant-calling, deepvariant, variant-calling (bcftools), joint-calling, structural-variant-calling, filtering-best-practices, variant-annotation, variant-normalization, vcf-basics, vcf-manipulation, vcf-statistics, consensus-sequences, clinical-interpretation ClawBio: vcf-annotator -- VEP + ClinVar + gnomAD annotation with ancestry-aware context variant-annotation -- Variant annotation pipeline

Differential Expression (Bulk RNA-seq)

bioSkills: differential-expression/ -- deseq2-basics, edger-basics, batch-correction, de-results, de-visualization, timeseries-de rna-quantification/ -- alignment-free-quant (Salmon/kallisto), featurecounts-counting, tximport-workflow, count-matrix-qc expression-matrix/ -- counts-ingest, gene-id-mapping, metadata-joins, sparse-handling ClawBio: rnaseq-de -- Full DE pipeline with QC, normalization, and visualization diff-visualizer -- Rich visualization and reporting for DE results

Single-Cell RNA-seq

bioSkills: single-cell/ -- preprocessing, clustering, batch-integration, cell-annotation, cell-communication, doublet-detection, markers-annotation, trajectory-inference, multimodal-integration, perturb-seq, scatac-analysis, lineage-tracing, metabolite-communication, data-io ClawBio: scrna-orchestrator -- Full Scanpy pipeline (QC, clustering, markers, annotation) scrna-embedding -- scVI-based latent embedding and batch integration

Spatial Transcriptomics

bioSkills: spatial-transcriptomics/ -- spatial-data-io, spatial-preprocessing, spatial-domains, spatial-deconvolution, spatial-communication, spatial-neighbors, spatial-statistics, spatial-visualization, spatial-multiomics, spatial-proteomics, image-analysis

Epigenomics

bioSkills: chip-seq/ -- peak-calling, differential-binding, motif-analysis, peak-annotation, chipseq-qc, chipseq-visualization, super-enhancers atac-seq/ -- atac-peak-calling, atac-qc, differential-accessibility, footprinting, motif-deviation, nucleosome-positioning methylation-analysis/ -- bismark-alignment, methylation-calling, dmr-detection, methylkit-analysis hi-c-analysis/ -- hic-data-io, tad-detection, loop-calling, compartment-analysis, contact-pairs, matrix-operations, hic-visualization, hic-differential ClawBio: methylation-clock -- Epigenetic age estimation

Pharmacogenomics & Clinical

bioSkills: clinical-databases/ -- clinvar-lookup, gnomad-frequencies, dbsnp-queries, pharmacogenomics, polygenic-risk, hla-typing, variant-prioritization, somatic-signatures, tumor-mutational-burden, myvariant-queries ClawBio: pharmgx-reporter -- PGx report from 23andMe/AncestryDNA (12 genes, 31 SNPs, 51 drugs) drug-photo -- Photo of medication to personalized PGx dosage card (via vision) clinpgx -- ClinPGx API for gene-drug data and CPIC guidelines gwas-lookup -- Federated variant lookup across 9 genomic databases gwas-prs -- Polygenic risk scores from consumer genetic data nutrigx_advisor -- Personalized nutrition from consumer genetic data

Population Genetics & GWAS

bioSkills: population-genetics/ -- association-testing (PLINK GWAS), plink-basics, population-structure, linkage-disequilibrium, scikit-allel-analysis, selection-statistics causal-genomics/ -- mendelian-randomization, fine-mapping, colocalization-analysis, mediation-analysis, pleiotropy-detection phasing-imputation/ -- haplotype-phasing, genotype-imputation, imputation-qc, reference-panels ClawBio: claw-ancestry-pca -- Ancestry PCA against SGDP reference panel

Metagenomics & Microbiome

bioSkills: metagenomics/ -- kraken-classification, metaphlan-profiling, abundance-estimation, functional-profiling, amr-detection, strain-tracking, metagenome-visualization microbiome/ -- amplicon-processing, diversity-analysis, differential-abundance, taxonomy-assignment, functional-prediction, qiime2-workflow ClawBio: claw-metagenomics -- Shotgun metagenomics profiling (taxonomy, resistome, functional pathways)

Genome Assembly & Annotation

bioSkills: genome-assembly/ -- hifi-assembly, long-read-assembly, short-read-assembly, metagenome-assembly, assembly-polishing, assembly-qc, scaffolding, contamination-detection genome-annotation/ -- eukaryotic-gene-prediction, prokaryotic-annotation, functional-annotation, ncrna-annotation, repeat-annotation, annotation-transfer long-read-sequencing/ -- basecalling, long-read-alignment, long-read-qc, clair3-variants, structural-variants, medaka-polishing, nanopore-methylation, isoseq-analysis

Structural Biology & Chemoinformatics

bioSkills: structural-biology/ -- alphafold-predictions, modern-structure-prediction, structure-io, structure-navigation, structure-modification, geometric-analysis chemoinformatics/ -- molecular-io, molecular-descriptors, similarity-searching, substructure-search, virtual-screening, admet-prediction, reaction-enumeration ClawBio: struct-predictor -- Local AlphaFold/Boltz/Chai structure prediction with comparison

Proteomics

bioSkills: proteomics/ -- data-import, peptide-identification, protein-inference, quantification, differential-abundance, dia-analysis, ptm-analysis, proteomics-qc, spectral-libraries ClawBio: proteomics-de -- Proteomics differential expression

Pathway Analysis & Gene Networks

bioSkills: pathway-analysis/ -- go-enrichment, gsea, kegg-pathways, reactome-pathways, wikipathways, enrichment-visualization gene-regulatory-networks/ -- scenic-regulons, coexpression-networks, differential-networks, multiomics-grn, perturbation-simulation

Immunoinformatics

bioSkills: immunoinformatics/ -- mhc-binding-prediction, epitope-prediction, neoantigen-prediction, immunogenicity-scoring, tcr-epitope-binding tcr-bcr-analysis/ -- mixcr-analysis, scirpy-analysis, immcantation-analysis, repertoire-visualization, vdjtools-analysis

CRISPR & Genome Engineering

bioSkills: crispr-screens/ -- mageck-analysis, jacks-analysis, hit-calling, screen-qc, library-design, crispresso-editing, base-editing-analysis, batch-correction genome-engineering/ -- grna-design, off-target-prediction, hdr-template-design, base-editing-design, prime-editing-design

Workflow Management

bioSkills: workflow-management/ -- snakemake-workflows, nextflow-pipelines, cwl-workflows, wdl-workflows ClawBio: repro-enforcer -- Export any analysis as reproducibility bundle (Conda env + Singularity + checksums) galaxy-bridge -- Access 8,000+ Galaxy tools from usegalaxy.org

Specialized Domains

bioSkills: alternative-splicing/ -- splicing-quantification, differential-splicing, isoform-switching, sashimi-plots, single-cell-splicing, splicing-qc ecological-genomics/ -- edna-metabarcoding, landscape-genomics, conservation-genetics, biodiversity-metrics, community-ecology, species-delimitation epidemiological-genomics/ -- pathogen-typing, variant-surveillance, phylodynamics, transmission-inference, amr-surveillance liquid-biopsy/ -- cfdna-preprocessing, ctdna-mutation-detection, fragment-analysis, tumor-fraction-estimation, methylation-based-detection, longitudinal-monitoring epitranscriptomics/ -- m6a-peak-calling, m6a-differential, m6anet-analysis, merip-preprocessing, modification-visualization metabolomics/ -- xcms-preprocessing, metabolite-annotation, normalization-qc, statistical-analysis, pathway-mapping, lipidomics, targeted-analysis, msdial-preprocessing flow-cytometry/ -- fcs-handling, gating-analysis, compensation-transformation, clustering-phenotyping, differential-analysis, cytometry-qc, doublet-detection, bead-normalization systems-biology/ -- flux-balance-analysis, metabolic-reconstruction, gene-essentiality, context-specific-models, model-curation rna-structure/ -- secondary-structure-prediction, ncrna-search, structure-probing

Data Visualization & Reporting

bioSkills: data-visualization/ -- ggplot2-fundamentals, heatmaps-clustering, volcano-customization, circos-plots, genome-browser-tracks, interactive-visualization, multipanel-figures, network-visualization, upset-plots, color-palettes, specialized-omics-plots, genome-tracks reporting/ -- rmarkdown-reports, quarto-reports, jupyter-reports, automated-qc-reports, figure-export ClawBio: profile-report -- Analysis profile reporting data-extractor -- Extract numerical data from scientific figure images (via vision) lit-synthesizer -- PubMed/bioRxiv search, summarization, citation graphs pubmed-summariser -- Gene/disease PubMed search with structured briefing

Database Access

bioSkills: database-access/ -- entrez-search, entrez-fetch, entrez-link, blast-searches, local-blast, sra-data, geo-data, uniprot-access, batch-downloads, interaction-databases, sequence-similarity ClawBio: ukb-navigator -- Semantic search across 12,000+ UK Biobank fields clinical-trial-finder -- Clinical trial discovery

Experimental Design

bioSkills: experimental-design/ -- power-analysis, sample-size, batch-design, multiple-testing

Machine Learning for Omics

bioSkills: machine-learning/ -- omics-classifiers, biomarker-discovery, survival-analysis, model-validation, prediction-explanation, atlas-mapping ClawBio: claw-semantic-sim -- Semantic similarity index for disease literature (PubMedBERT) omics-target-evidence-mapper -- Aggregate target-level evidence across omics sources

Environment Setup

These skills assume a bioinformatics workstation. Common dependencies:

# Python
pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata scanpy mygene

# R/Bioconductor
Rscript -e 'BiocManager::install(c("DESeq2","edgeR","Seurat","clusterProfiler","methylKit"))'

# CLI tools (Ubuntu/Debian)
sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools

# CLI tools (macOS)
brew install samtools bcftools blast minimap2 bedtools

# Or via Conda (recommended for reproducibility)
conda install -c bioconda samtools bcftools blast minimap2 bedtools fastp kraken2

Pitfalls

• The fetched skills are NOT in Hermes SKILL.md format. They use their own structure (bioSkills: code pattern cookbooks; ClawBio: README + Python scripts). Read them as expert reference material.
• bioSkills are reference guides -- they show correct parameters and code patterns but aren't executable pipelines.
• ClawBio skills are executable -- many have --demo flags and can be run directly.
• Both repos assume bioinformatics tools are installed. Check prerequisites before running pipelines.
• For ClawBio, run pip install -r requirements.txt in the cloned repo first.
• Genomic data files can be very large. Be mindful of disk space when downloading reference genomes, SRA datasets, or building indices.

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Ported to hakase from Hermes Agent (MIT). Original: Bioinformatics gateway skill by Hermes Agent (MIT).