Skills

One row per skill. Each skill's SKILL.md is the authoritative description: its frontmatter gives the name and trigger, and its body gives instructions, inputs, outputs and quality gates. The sources are under skills/.

Omics analysis

Skill	Use when	Main result
bioinformatics-project	Starting, reorganizing, or reproducibility-hardening a bioinformatics project.	Project layout, pinned environment, task records, hypothesis register, restartable drivers, provenance, and sharing metadata.
bio-foundation-housekeeping	Defining metadata schemas or adding a queryable data catalog.	Generated LinkML/Pydantic models, cross-record validation, normalized Parquet tables, fixtures, and a DuckDB catalog.
exploratory-data-analysis	Inspecting an unfamiliar scientific data file before choosing a workflow.	A Markdown report covering file type, structure, quality issues, and downstream analysis options.
bio-reads-qc-mapping	Ingesting raw reads, trimming or filtering them, and mapping reads to references or assemblies.	Per-sample trimmed reads, fastp reports for short reads, SAM alignments when a reference is given, a run manifest, and a mapping-status table.
bio-assembly-qc	Assembling QC-passed reads into isolate or metagenome contigs and checking contiguity.	Per-sample contigs.fasta, QUAST or MetaQUAST report.tsv, a run manifest, and QuickClade domain routing.
tracking-taxonomy-updates	Comparing NCBI, GTDB, ICTV, or eukaryotic taxonomy releases, or assigning taxonomy to sequences.	Versioned change and conflict report, QuickClade domain_routing.tsv, and GTDB-Tk, EukCC, vConTACT3, or GVClass assignments.
bio-binning-qc	Binning a metagenome assembly with QuickBin or scoring bin completeness, contamination, and chimerism.	Bins, QuickClade domain routing, bin_metrics.tsv with CheckM2, GUNC, or EukCC scores, and GTDB-Tk taxonomy.
bio-gene-calling	Calling CDS in prokaryotic, viral, or eukaryotic assemblies, or counting tRNA and rRNA genes.	Gene models, protein and coding sequences per assembly (BRAKER outputs for eukaryotes), an ncRNA_census.tsv of tRNA and rRNA counts, and gene metrics.
bio-annotation	Assigning function and taxonomy from sequence homology.	Annotation and taxonomy Parquet tables, marker_census.tsv, a family copy-number matrix, and discovery_candidates.tsv.
bio-fasta-database-curator	Preparing sequence databases for BLAST, DIAMOND, MMseqs2, HMMER, pyhmmer, or custom reference searches.	Curated FASTA/FAA files, stable headers, deduplicated records, mapping tables, and database statistics.
bio-phylogenomics	Inferring marker-gene phylogenies, placing genomes, choosing substitution models, or checking tree support.	Per-marker trimmed alignments, ML trees, support tables, closest_relatives.tsv, and fetched relative genomes and proteomes.
bio-interdomain-hgt	Testing interdomain horizontal gene transfer and donor direction.	Homology, context, contamination, and per-gene phylogenetic evidence for candidate transfers.
bio-protein-clustering-pangenome	Clustering proteins into orthogroups, or comparing gene-family copy number and core/accessory content.	Orthogroups, presence/absence and copy-number matrices, family fold-change table, conserved neighborhoods, and marker and ncRNA censuses.
bio-structure-annotation	Adding structure-based evidence to protein interpretation.	Predicted or searched structures, fold-level annotations, and confidence notes.
bio-viromics	Detecting, classifying, and QCing viral contigs.	Viral calls, quality summaries, taxonomy evidence, and candidate discovery tables.
bio-stats-ml-reporting	Testing hypotheses, training classifiers, or rolling up discovery evidence from biological results.	Models and metrics.tsv, prediction validation, comparative_axes_summary.tsv, discovery_summary.tsv, and report.md.
bio-prefect-dask-nextflow	Designing a local, distributed, or Slurm-backed bioinformatics workflow.	Engine recommendation with rationale, runnable Prefect+Dask or Nextflow scaffold, per-step resource plan, and validation plan.
bio-workflow-methods-docwriter	Turning Nextflow, Snakemake, or CWL run artifacts into a Methods section.	Schema-validated run_manifest.yaml and METHODS.md with exact commands, versions, parameters, QC, and outputs.
bio-logic	Auditing scientific reasoning, study design, bias, or strength of evidence.	A structured critique with uncertainty, alternative explanations, and follow-up checks.

Literature and metadata

Skill	Use when	Main result
polars-dovmed	Searching PMC Open Access or bioRxiv full text via the hosted API or parquet.	A run directory with query.json, raw responses, and timings, plus a paper list with relevance notes.
arxiv-search	Finding CS, math, physics, statistics, or quantitative-biology preprints, or resolving arXiv IDs.	JSON search results from the arXiv API and optional Markdown notes per arXiv ID.
biorxiv-search	Scanning bioRxiv preprints by date range, category, or author, or looking up bioRxiv DOIs.	JSON matches from a bounded date window, keyword-filtered locally, with scan counts and truncation warnings.
crossref-lookup	Validating DOIs or matching titles to citation metadata.	Crossref records, DOI matches, and bibliography cleanup evidence.
public-db-lookup	Fetching a record from UniProt, NCBI, MGnify, InterPro, AlphaFold DB, STRING, or ENA.	A compact JSON envelope with bounded records, counts, and an optional raw-response file.
scientific-impact-assessment	Comparing papers, journals, or literature shortlists by influence.	OpenAlex citation counts and history, curated journal impact factors, and optional Altmetric data.
pdf-to-md	Converting papers, PDFs, or office documents into analysis-ready Markdown.	Clean Markdown and, for papers, structured article and section-audit artifacts.

Writing and review

Skill	Use when	Main result
scientific-writing	Drafting or revising manuscript sections, proposal narratives, or rebuttals, or running a clarity review.	Draft or revised prose within the evidence, severity-tagged findings, a citation audit, and unresolved evidence gaps.
csag-extraction	Converting manuscripts into structured Conditional Scientific Argumentation Graphs.	Schema-valid claim/evidence/inference graphs with TextSpan grounding, validation reports, and paper-grounded Q&A items.
manuscript-review-council	Running a journal-style peer review, or checking a revision or rebuttal against prior objections.	Role-separated reviewer reports, an adjudication log, an editor meta-review with recommendation, and a validated review bundle.
proposal-review	Scoring an AI/ML, computational-biology, or bioscience proposal for a funding decision.	Structured review, risk register, weighted scorecard, funding recommendation with conditions, and questions for the PI.
ai-scientist-evaluator	Evaluating finished outputs from one or more AI scientists.	A scored audit of rigor, reproducibility, novelty, task completion, and publication readiness.

Visualization and notebooks

Skill	Use when	Main result
notebooks	Building or converting reproducible marimo or Jupyter notebooks.	A fully executed notebook with embedded figures and clear analysis flow.
beautiful-data-viz	Making, restyling, or reviewing any plot, chart, figure, dashboard, or data visual.	Greyscale-first PNG, SVG, PDF, or HTML figures, color only to encode information, and reproducible plotting code.
plotly-dashboard-skill	Building interactive Plotly Dash dashboards.	Dash app scaffold with layout, callbacks, one registered figure template, and a README with usage notes.