bioinformatics

# 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): ```bash # 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: ```bash # 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-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: ```bash # 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.