hermes-agent/optional-skills/research/bioinformatics/SKILL.md

name	description	version	platforms	metadata
bioinformatics	Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.	1.0.0	linux macos	hermes tags category bioinformatics genomics sequencing biology research science research

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.

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 → 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.