bioinformatics – Data & Science skill for AI agents

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 ~/.hermes/cache/scratch/bioSkills

   # ClawBio (runnable pipelines)
   git clone --depth 1 https://github.com/ClawBio/ClawBio.git ~/.hermes/cache/scratch/ClawBio
   

3. Read the specific skill:

   # bioSkills — each skill is at: <category>/<skill-name>/SKILL.md
   cat ~/.hermes/cache/scratch/bioSkills/variant-calling/gatk-variant-calling/SKILL.md

   # ClawBio — each skill is at: skills/<skill-name>/
   cat ~/.hermes/cache/scratch/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-work

… (full content is in the download package)