Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches
Real data. Real impact.
Emerging
Developers
Per week
Excellent
Skills give you superpowers. Install in 30 seconds.
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.
◆ 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.
# 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
# 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
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)
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
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
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
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
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
bioSkills: experimental-design/ — power-analysis, sample-size, batch-design, multiple-testing
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
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
--demopip install -r requirements.txtMIT
mkdir -p ~/.hermes/skills/research/bioinformatics && curl -o ~/.hermes/skills/research/bioinformatics/SKILL.md https://raw.githubusercontent.com/NousResearch/hermes-agent/main/optional-skills/research/bioinformatics/SKILL.md
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