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 /tmp/bioSkills

   # ClawBio (runnable pipelines)
   git clone --depth 1 https://github.com/ClawBio/ClawBio.git /tmp/ClawBio
   ```
3. Read the specific skill:
   ```bash
   # 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-analys