# ONT Ecosystem Skill Reference > Auto-generated by `ont_docgen.py skills` - v3.2.2 This document consolidates all available skills with their frontmatter metadata. ## Quick Reference Table | Skill | Description | Pipeline Stage | Script | |-------|-------------|----------------|--------| | [aldy](#aldy) | Aldy star-allele caller wrapper for CYP2D6 and other complex... | - | - | | [alt-contig-rescue](#alt-contig-rescue) | Recover reads mis-mapped to GRCh38 ALT haplotype contigs (HS... | - | - | | [auto-visualize](#auto-visualize) | Automatically discover, synthesize, visualize, and publish p... | - | - | | [barcode-oligos](#barcode-oligos) | Analyze, visualize, and manage duplexed barcode oligos for S... | - | - | | [batch-run](#batch-run) | Run SMA-seq pipeline stages across multiple experiments with... | - | - | | [cas9-enrichment](#cas9-enrichment) | >- | - | - | | [cas9-guide-mapper](#cas9-guide-mapper) | Map CRISPR/Cas9 guide RNA sequences to a reference genome or... | - | - | | [cas9-panel-eval](#cas9-panel-eval) | Comprehensive panel evaluation of PacBio Cas9-targeted seque... | - | - | | [check-submission](#check-submission) | [DEPRECATED → use lab-submission-check --paper smaseq-ng] Le... | - | - | | [cleanup-scripts](#cleanup-scripts) | Identify and clean up draft, backup, and redundant Python sc... | - | - | | [comprehensive-analysis](#comprehensive-analysis) | Comprehensive ONT sequencing analysis with KDE distributions... | - | - | | [consolidate](#consolidate) | Package up session changes, sync CLAUDE.md sections, verify ... | - | - | | [cross-registry-audit](#cross-registry-audit) | Run a broken-link audit across every lab YAML/SQLite registr... | - | - | | [custom-paper-visualizations](#custom-paper-visualizations) | Generate publication-quality scientific visualizations for l... | - | - | | [data-skill](#data-skill) | Analyze sequencing data files (BAM, FASTQ, POD5). Use when t... | - | - | | [dedup-auditor](#dedup-auditor) | Audit Python scripts for duplicated logic, copy-paste drift,... | - | - | | [demux-analysis](#demux-analysis) | Run CLC barcode demultiplexing and QC analysis on SMA-seq ex... | - | - | | [dorado-bench-v2](#dorado-bench-v2) | Oxford Nanopore basecalling with Dorado - automatic model ma... | - | - | | [end-reason](#end-reason) | Oxford Nanopore read end reason QC analysis. Analyzes sequen... | - | - | | [experiment-db](#experiment-db) | SQLite database for tracking nanopore experiments with fast ... | - | - | | [fast-subsample](#fast-subsample) | Fast BAM subsampling using SMAI index with clustered I/O. Su... | - | - | | [gene-coordinate-validator](#gene-coordinate-validator) | Look up, validate, and cross-reference gene coordinates from... | - | - | | [gg-pipeline](#gg-pipeline) | Run the full Golden Gate QC pipeline end-to-end. Chains gg e... | - | - | | [git-sync](#git-sync) | Commit and push changes in sma-seq-workspace and smaseq-qc s... | - | - | | [golden-gate-assembly](#golden-gate-assembly) | Golden Gate cloning assembly design for combinatorial varian... | - | - | | [greatlakes-sync](#greatlakes-sync) | Synchronize experiment data between Great Lakes HPC and loca... | - | - | | [health-check](#health-check) | System health monitoring for ONT Ecosystem. Verifies Python ... | - | - | | [igv-batch](#igv-batch) | Batch IGV report generation for multiple patients and gene r... | - | - | | [igv-report](#igv-report) | Generate strand-specific IGV HTML reports with coordinate sa... | - | - | | [ingest-transcripts](#ingest-transcripts) | Ingest Tactiq meeting transcripts into the Athey Lab Wiki wi... | - | - | | [lab-doctor](#lab-doctor) | Comprehensive lab health check with a single 0-100 score. Ag... | - | - | | [lab-drive](#lab-drive) | Search and mine the lab Google Drive corpus (via rclone gdri... | - | - | | [lab-fixall](#lab-fixall) | End-of-session lab-wide cleanup sweep. Refreshes canonical R... | - | - | | [lab-inbox](#lab-inbox) | Mine Gmail (gregfar@umich.edu) for paper-relevant intelligen... | - | - | | [lab-manuscript](#lab-manuscript) | Build, check, and maintain any lab manuscript registered in ... | - | - | | [lab-paper-status](#lab-paper-status) | Cross-paper status dashboard for all lab manuscripts. Reads ... | - | - | | [lab-papers-bump](#lab-papers-bump) | Propose lab-render.yml SHA-pin updates as PRs across all pap... | - | - | | [lab-query](#lab-query) | Query the lab knowledge index — search across lab-wiki, lab-... | - | - | | [lab-refs](#lab-refs) | Agent-driven curator for the lab reference library. Use when... | - | - | | [lab-site-template](#lab-site-template) | Generate a consistent GitHub Pages landing page for any lab ... | - | - | | [lab-status](#lab-status) | Show a single-screen lab dashboard — atom adoption + README ... | - | - | | [lab-submission-check](#lab-submission-check) | Journal-aware pre-submission checklist for any lab manuscrip... | - | - | | [lab-textbook-search](#lab-textbook-search) | | | - | - | | [lab-transcripts](#lab-transcripts) | Paper-centric view of the Athey Lab wiki's meeting and decis... | - | - | | [lab-wiki](#lab-wiki) | Operate the Athey Lab Wiki — ingest sources into structured ... | - | - | | [lab-wiki-calendar](#lab-wiki-calendar) | Pre-create wiki transcript pages from upcoming Google Calend... | - | - | | [lab-wiki-tactiq](#lab-wiki-tactiq) | Ingest Tactiq meeting transcripts from Google Drive into the... | - | - | | [lab-workspace](#lab-workspace) | Activate, pin, inspect, and health-check workspaces (project... | - | - | | [library-prep-comparison](#library-prep-comparison) | Compare different SMA-seq library preparation methods (e.g.,... | - | - | | [lifecycle](#lifecycle) | Experiment lifecycle tracking and pipeline orchestration | - | - | | [link-health-monitor](#link-health-monitor) | Continuous link-health monitor across lab repos. Checks dail... | infrastructure | - | | [locus-igv-builder](#locus-igv-builder) | Build comprehensive IGV sessions for any complex genomic loc... | - | - | | [manuscript](#manuscript) | Generate publication-quality figures and tables from ONT seq... | - | - | | [manuscript-status](#manuscript-status) | Show SMA-seq manuscript completion status — word counts, fig... | - | - | | [menu](#menu) | Interactive menu walker that shows all lab functionality as ... | - | - | | [morning](#morning) | Session-start orientation. Runs the lab-status text dashboar... | - | - | | [multi-locus-enrichment](#multi-locus-enrichment) | >- | - | - | | [onboard-member](#onboard-member) | Generate a complete Athey Lab onboarding bundle for a new me... | - | - | | [ont-align](#ont-align) | Oxford Nanopore alignment with minimap2/dorado, reference ge... | - | - | | [ont-experiments-v2](#ont-experiments-v2) | Enhanced Oxford Nanopore experiment management with event-so... | - | - | | [ont-explorer](#ont-explorer) | Comprehensive experiment exploration - metadata collection, ... | - | - | | [ont-lifecycle](#ont-lifecycle) | Experiment lifecycle tracking with dependency graphs, stage ... | - | - | | [ont-metadata](#ont-metadata) | Extract and manage metadata from Oxford Nanopore sequencing ... | - | - | | [ont-monitor](#ont-monitor) | Real-time and retrospective Oxford Nanopore sequencing run m... | - | - | | [ont-pipeline](#ont-pipeline) | Oxford Nanopore multi-step workflow orchestration with unifi... | - | - | | [ont-public-data](#ont-public-data) | Discover, stream, and analyze public ONT datasets from S3 wi... | - | - | | [ont-welcome](#ont-welcome) | Session start welcome with context-aware suggestions. Presen... | - | - | | [overnight-ingest](#overnight-ingest) | Automated overnight maintenance for the Athey Lab Wiki — syn... | - | - | | [pacbio-igv-reports](#pacbio-igv-reports) | Generate standalone HTML IGV reports from PacBio HiFi or ONT... | - | - | | [pacbio-qscore](#pacbio-qscore) | Per-library Q-score distribution, calibration, and error-rat... | - | - | | [paralog-discriminator](#paralog-discriminator) | Discriminate reads between high-identity paralogs/pseudogene... | - | - | | [pharmvar-genotype](#pharmvar-genotype) | Pharmacogenomic star allele genotyping using PharmVar haplot... | - | - | | [pipeline](#pipeline) | SMA-seq MMID pipeline library providing modular L0-L6 layers... | - | - | | [pipeline-run](#pipeline-run) | Run the full SMA-seq analysis pipeline on one or more experi... | - | - | | [pipeline-status](#pipeline-status) | Check SMA-seq pipeline completion status across all experime... | - | - | | [plan-reconciler](#plan-reconciler) | Detect and optionally flip stale checkboxes in superpowers i... | - | - | | [plugin-doctor](#plugin-doctor) | Health-check and auto-fix for Claude Code plugins, skills, a... | - | - | | [project-walkthrough](#project-walkthrough) | Interactive content-first questionnaire walkthrough for a la... | - | - | | [propose](#propose) | Scan the full SMA-seq workspace and propose prioritized anal... | - | - | | [pypgx](#pypgx) | PyPGx pharmacogenomic genotyping wrapper. Runs the long-read... | - | - | | [qc-advisor](#qc-advisor) | AI-powered QC analysis for Oxford Nanopore sequencing. Provi... | - | - | | [qscore-calibration](#qscore-calibration) | Comprehensive Q-score calibration and discriminability analy... | - | - | | [reflect](#reflect) | Process queued learnings and apply them to CLAUDE.md. Captur... | - | - | | [registry-browser](#registry-browser) | Interactive HTML browser for the ONT experiment registry wit... | - | - | | [registry-explorer](#registry-explorer) | Explore and search the ONT experiment registry with advanced... | - | - | | [registry-scrutinize](#registry-scrutinize) | Audit, validate, and fix ONT experiment registry entries wit... | - | - | | [registry-server](#registry-server) | Flask API server for federated experiment tracking with mult... | - | - | | [registry-unified](#registry-unified) | Build a single sortable/filterable HTML view of all lab expe... | - | - | | [registry-validator](#registry-validator) | Validate SMA registry referential integrity across all 6 sub... | - | - | | [repeat-expansion-analyzer](#repeat-expansion-analyzer) | Size trinucleotide, tetranucleotide, pentanucleotide, and he... | - | - | | [repo-analyzer](#repo-analyzer) | Analyze lab paper/project repositories for gaps, completenes... | - | - | | [seed-project-ledgers](#seed-project-ledgers) | Step through lab projects one at a time, bootstrapping each ... | - | - | | [skill-doctor](#skill-doctor) | Tier-1 health auditor for the lab's 84-skill ecosystem. Lint... | - | - | | [skill-maker](#skill-maker) | Create, update, and manage Claude skills automatically. Use ... | - | - | | [skill-orchestration](#skill-orchestration) | Intelligent skill routing for ONT Ecosystem. Finds the right... | - | - | | [skill-recommender](#skill-recommender) | Tier-2 agentic auditor for the lab's skill ecosystem. Reads ... | - | - | | [sma-analysis](#sma-analysis) | SMA-seq multi-experiment alignment-based classification and ... | - | - | | [sma-igv-reports](#sma-igv-reports) | Generate standalone HTML IGV reports for SMA-seq experiments... | - | - | | [sma-launcher](#sma-launcher) | Discover and run SMA-seq analysis tools. Use when the user d... | - | - | | [sma-pipeline](#sma-pipeline) | Full SMA-seq pipeline orchestrator with database initializat... | - | - | | [sma-prep](#sma-prep) | SMA-seq library prep and reference management. Create refere... | - | - | | [sma-reference](#sma-reference) | SMA-seq reference sequence management. Create, validate, ind... | - | - | | [sma-seq](#sma-seq) | Modular SMA-seq analysis components for database operations,... | - | - | | [sma-viz](#sma-viz) | Multi-reference SMA-seq visualization. Subsamples reads, ali... | - | - | | [sma-config-builder](#sma-config-builder) | Interactive web UI for building and editing SMA-seq configur... | - | - | | [smaseq-qc-dev](#smaseq-qc-dev) | Run tests, lint, and validate the smaseq-qc package after co... | - | - | | [tapestation-sampling](#tapestation-sampling) | Predict CRISPR/Cas9 enrichment yield from TapeStation DNA qu... | - | - | | [test-lib](#test-lib) | Run and manage the test suite for SMA-seq lib/ modules. Supp... | - | - | | [viz-automation](#viz-automation) | | - | - | | [workspace-porter](#workspace-porter) | Export and restore Claude Code workspace configuration acros... | - | - | ## Pipeline Stage Legend | Symbol | Stage | |--------|-------| | r | Raw data processing (basecalling) | | sigma | QC analysis (end reasons) | | lambda | Alignment | | - | General utility | --- ## Skill Details ### aldy **Description:** Aldy star-allele caller wrapper for CYP2D6 and other complex pharmacogenes. Standardises the lab's hg38 + pacbio-hifi-targeted long-read protocol, batches multi-sample/multi-gene calls, parses the .aldy text output into structured JSON, and runs alongside pypgx for cross-call validation. Use for star-allele genotyping from long-read or HiFi BAMs, especially when you want a second independent diplotyper to compare against pypgx. | Property | Value | |----------|-------| | SKILL.md | `../skills/aldy/SKILL.md` | # aldy Wrapper around `aldy` (https://github.com/0xTCG/aldy) — Bayesian star-allele caller specialised for highly polymorphic genes (CYP2D6 in particular). Used in the lab as an independent second-opinion against `pypgx` for diplotype calls; agreement is a strong QC signal. [Full documentation](../skills/aldy/SKILL.md) --- ### alt-contig-rescue **Description:** Recover reads mis-mapped to GRCh38 ALT haplotype contigs (HSCHR*) and | Property | Value | |----------|-------| | SKILL.md | `../skills/alt-contig-rescue/SKILL.md` | > **Prerequisite:** Run `/gene-coordinate-validator` to verify gene coordinates before using this skill. Wrong coordinates silently corrupt all downstream outputs. # ALT Contig Read Rescue Recover reads that GRCh38 ALT haplotype scaffolds have stolen from a primary assembly target locus. Realign all reads (primary + ALT) to the primary locus reference for unified analysis. [Full documentation](../skills/alt-contig-rescue/SKILL.md) --- ### auto-visualize **Description:** Automatically discover, synthesize, visualize, and publish paper/project repository information as PNG/PDF/atlas bundles with README links. Use when a user asks to continue improving visualizations, create PDF outputs, refresh a paper/project repo, synthesize project information, or run automatic visualization across lab-infrastructure paper and project repos. | Property | Value | |----------|-------| | SKILL.md | `../skills/auto-visualize/SKILL.md` | # Auto Visualize Automatically generate GitHub-ready visualization bundles for lab paper and project repositories. [Full documentation](../skills/auto-visualize/SKILL.md) --- ### barcode-oligos **Description:** Analyze, visualize, and manage duplexed barcode oligos for SMA-seq library | Property | Value | |----------|-------| | SKILL.md | `../skills/barcode-oligos/SKILL.md` | # Barcode Oligos Skill Comprehensive tool for managing duplexed barcode oligos used in SMA-seq library preparation with Golden Gate assembly. [Full documentation](../skills/barcode-oligos/SKILL.md) --- ### batch-run **Description:** Run SMA-seq pipeline stages across multiple experiments with validation. Supports selective re-runs, dry-run mode, and automatic artifact validation. Use when applying the same pipeline stage(s) to a cohort of experiments, especially after a config change that needs to propagate across many runs at once. | Property | Value | |----------|-------| | SKILL.md | `../skills/batch-run/SKILL.md` | # Batch Run — Multi-Experiment Pipeline Runner Run one or more pipeline stages across selected experiments with built-in validation. [Full documentation](../skills/batch-run/SKILL.md) --- ### cas9-enrichment **Description:** >- | Property | Value | |----------|-------| | SKILL.md | `../skills/cas9-enrichment/SKILL.md` | > **Prerequisite:** Run `/gene-coordinate-validator` to verify gene coordinates before using this skill. Wrong coordinates silently corrupt all downstream outputs. > > **Downstream analysis (v1.6 default):** After this skill produces `cas9_analysis/per_patient/*/grna_detections.tsv`, run **`/cas9-panel-eval`** for the full panel evaluation. v1.6 delivers: > - **Anchored model** `z = c_l × (x_i × x_j)` where `c_l` = z of the observed max-efficiency fragment per library (anchored to a concrete measurement, not a free parameter) > - **True fragment-spanning counts** (reads matching BOTH cuts within ±2 bp) > - **15 top-level figures** (PNG+PDF each): schematic-zoomed with anchor highlights, pair-product matrix, within-library fragment bars, per-region 2×2 bipartite heatmaps, fit diagnostic, library anchors, A/B comparisons, + 9 more > - **Per-cut dossier figure per gRNA** (ref sequence ±25bp color-coded, per-lib reads, offset pileup, metadata) > - **grna_summary.html** (sortable/filterable per-gRNA table) > - **panel_recommendations.tsv** — ranked design opportunities for unobserved (start × end) pairs > - **panel_eval_report.pdf** — single multi-page PDF (cover + all figures + all dossiers) > - **README.md + MANIFEST.txt + bundle.zip** — one-shot deliverable > See `cas9-targeted-sequencing/content/protocols/panel-evaluation-workflow.md` for full protocol. # Cas9 Targeted Enrichment Analysis Comprehensive de novo analysis of CRISPR/Cas9 enrichment sequencing data. The pipeline builds understanding from the ground up: raw alignments → cut site detection → gRNA extraction → fragment characterization → gene annotation. [Full documentation](../skills/cas9-enrichment/SKILL.md) --- ### cas9-guide-mapper **Description:** Map CRISPR/Cas9 guide RNA sequences to a reference genome or locus. Finds | Property | Value | |----------|-------| | SKILL.md | `../skills/cas9-guide-mapper/SKILL.md` | > **Prerequisite:** Run `/gene-coordinate-validator` to verify gene coordinates before using this skill. Wrong coordinates silently corrupt all downstream outputs. # Cas9 Guide Mapper Map any set of CRISPR gRNA sequences to a reference, identify cut positions, group by region, calculate expected fragments, and generate IGV-ready BED tracks. > **Companion skills in the Cas9 pipeline (v1.6 workflow):** > - **Before wet lab** (panel design): this skill — map designed gRNAs to reference > - **After sequencing** (de novo detection): `/cas9-enrichment` > - **After detection** (panel evaluation): `/cas9-panel-eval` v1.6 — anchored-`c_l` per-guide efficiency fit, fragment-spanning counts, 15 figures + per-cut dossiers, panel_recommendations.tsv for design-gap scoring, unified multi-page PDF. Use the BED produced by this skill as the `--panel-bed` input to `/cas9-panel-eval`. [Full documentation](../skills/cas9-guide-mapper/SKILL.md) --- ### cas9-panel-eval **Description:** Comprehensive panel evaluation of PacBio Cas9-targeted sequencing: reconstructs the designed gRNA panel from /cas9-enrichment detections, builds per-cut forensic dossiers (±5bp offset pileup, PAM geometry, protospacer, cleavage diagrams), validates SMRTbell fwd/rev chemistry, fits a fragment-level log-linear system ranking per-guide cleavage-ligation efficiency, computes gauge-free A/B variant comparisons, and renders publication-ready annotated genome schematics. Use AFTER /cas9-enrichment has generated per-patient grna_detections.tsv. Triggers on: evaluate panel, rank gRNAs, A vs B comparison, fragment fit, cleavage-ligation efficiency, compare guide design, reconstruct panel, genome schematic for Cas9. | Property | Value | |----------|-------| | SKILL.md | `../skills/cas9-panel-eval/SKILL.md` | > **Prerequisite 1:** Run `/gene-coordinate-validator` to verify gene coordinates. > **Prerequisite 2:** Run `/cas9-enrichment` to produce `cas9_analysis/per_patient/*/grna_detections.tsv` (the authoritative per-library cut-to-spacer mapping with `mismatches` column). # Cas9 Panel Evaluation — end-to-end analytics for PacBio Cas9-targeted sequencing [Full documentation](../skills/cas9-panel-eval/SKILL.md) --- ### check-submission **Description:** [DEPRECATED → use lab-submission-check --paper smaseq-ng] Legacy Nature Genetics pre-submission checklist for the SMA-seq manuscript. Superseded by the journal-aware lab-submission-check skill which handles 4+ journals via YAML rulesets. | Property | Value | |----------|-------| | SKILL.md | `../skills/check-submission/SKILL.md` | # Pre-Submission Checklist (DEPRECATED) > ⚠ **This skill is deprecated.** Use `lab-submission-check --paper smaseq-ng` instead. > The new skill is journal-aware (Nature Genetics, Scientific Data, Clinical Pharmacology > & Therapeutics, UM Rackham thesis) and reads paper metadata from `lab-papers/papers.yaml` > automatically. Maintained as a 30-day alias for compatibility. --- Run a comprehensive Nature Genetics compliance check before manuscript submission. [Full documentation](../skills/check-submission/SKILL.md) --- ### cleanup-scripts **Description:** Identify and clean up draft, backup, and redundant Python scripts in the SMA analysis workspace. Classifies files by safety level and provides delete/archive/keep recommendations. Use when the SMA workspace has accumulated draft/backup scripts (e.g., *.bak, *_v2.py, abandoned exploration files) and the user wants a triage pass before deletion. | Property | Value | |----------|-------| | SKILL.md | `../skills/cleanup-scripts/SKILL.md` | # Script Cleanup Identify draft, backup, and redundant scripts that can be safely removed to reduce workspace clutter. [Full documentation](../skills/cleanup-scripts/SKILL.md) --- ### comprehensive-analysis **Description:** Comprehensive ONT sequencing analysis with KDE distributions, end-reason | Property | Value | |----------|-------| | SKILL.md | `../skills/comprehensive-analysis/SKILL.md` | # Comprehensive Analysis Skill Generates publication-quality visualizations and comprehensive analysis of Oxford Nanopore sequencing experiments with consistent end-reason color coding and intelligent data sampling. [Full documentation](../skills/comprehensive-analysis/SKILL.md) --- ### consolidate **Description:** Package up session changes, sync CLAUDE.md sections, verify hooks, update memory, and audit the ecosystem. ALWAYS pushes new/orphaned skills to the repo — skills must never exist only locally. Discovers skills across all repos, compares versions, and integrates everything into the canonical ont-ecosystem repo. Use when ending a working session, before a release, or when memory/CLAUDE.md/skills feel out of sync across repos. | Property | Value | |----------|-------| | SKILL.md | `../skills/consolidate/SKILL.md` | # Session Consolidation & Ecosystem Audit Package up all changes, then discover, compare, and integrate skills across all repos. **No skill should remain local-only** — every skill gets pushed to the canonical repo. [Full documentation](../skills/consolidate/SKILL.md) --- ### cross-registry-audit **Description:** Run a broken-link audit across every lab YAML/SQLite registry (ont-registry, sma-registry, papers.yaml, lab-locations.yaml) in one pass. Generalizes the per-source check that registry-scrutinize does for ONT only. Use when you suspect path rot has crept in across the ecosystem (e.g., after a directory tree was moved), when onboarding to the lab and want a fresh hygiene baseline, or as a periodic CI check to catch drift before it causes silent failures downstream. | Property | Value | |----------|-------| | SKILL.md | `../skills/cross-registry-audit/SKILL.md` | # /cross-registry-audit — broken-link sweep across all lab registries [Full documentation](../skills/cross-registry-audit/SKILL.md) --- ### custom-paper-visualizations **Description:** Generate publication-quality scientific visualizations for lab papers. Automates figure generation, README updates, and Git commits across all papers in the registry. | Property | Value | |----------|-------| | SKILL.md | `../skills/custom-paper-visualizations/SKILL.md` | # Custom Paper Visualizations Generate publication-quality scientific figures for lab papers using reproducible Python scripts. This is the core infrastructure that scales scientific visualization across the lab. [Full documentation](../skills/custom-paper-visualizations/SKILL.md) --- ### data-skill **Description:** Analyze sequencing data files (BAM, FASTQ, POD5). Use when the user asks | Property | Value | |----------|-------| | SKILL.md | `../skills/data-skill/SKILL.md` | # Data Skill Analyze sequencing data files (BAM, FASTQ, POD5). ## Integration Run through ont-experiments for provenance tracking (Pattern B): ```bash ont_experiments.py run data_skill --json results.json ``` Or standalone: ```bash python skills/data-skill/scripts/data_skill.py /path/to/input --json results.json ``` [Full documentation](../skills/data-skill/SKILL.md) --- ### dedup-auditor **Description:** Audit Python scripts for duplicated logic, copy-paste drift, and redundant backup files. Identifies functions that appear in multiple files with minor variations. Use when investigating whether multiple SMA scripts have drifted into copy-paste variants of the same helper logic — typically before extracting shared utilities or refactoring. | Property | Value | |----------|-------| | SKILL.md | `../skills/dedup-auditor/SKILL.md` | # Script Deduplication Auditor Find duplicated logic across Python scripts in the SMA analysis workspace. [Full documentation](../skills/dedup-auditor/SKILL.md) --- ### demux-analysis **Description:** Run CLC barcode demultiplexing and QC analysis on SMA-seq experiments. | Property | Value | |----------|-------| | SKILL.md | `../skills/demux-analysis/SKILL.md` | # CLC Demultiplexing Workflow [Full documentation](../skills/demux-analysis/SKILL.md) --- ### dorado-bench-v2 **Description:** Oxford Nanopore basecalling with Dorado - automatic model management, | Property | Value | |----------|-------| | SKILL.md | `../skills/dorado-bench-v2/SKILL.md` | # Dorado-Bench v2 - ONT Basecalling Basecalling toolkit with automated model management, provenance tracking, and support for local and HPC execution. [Full documentation](../skills/dorado-bench-v2/SKILL.md) --- ### end-reason **Description:** Oxford Nanopore read end reason QC analysis. Analyzes sequencing quality, | Property | Value | |----------|-------| | SKILL.md | `../skills/end-reason/SKILL.md` | # End Reason Analysis - ONT QC Analyze Oxford Nanopore read end reasons for quality assessment and adaptive sampling efficiency. ## Integration Run through ont-experiments for provenance tracking: ```bash ont_experiments.py run end_reasons exp-abc123 --json results.json --plot qc.png ``` Or standalone: ```bash python3 end_reason.py /path/to/data --json results.json ``` [Full documentation](../skills/end-reason/SKILL.md) --- ### experiment-db **Description:** SQLite database for tracking nanopore experiments with fast SQL queries | Property | Value | |----------|-------| | SKILL.md | `../skills/experiment-db/SKILL.md` | # Experiment Database Skill SQLite database for tracking nanopore sequencing experiments. Complements the YAML-based ont-experiments-v2 registry by providing fast SQL-based queries for statistics and end reason distributions. [Full documentation](../skills/experiment-db/SKILL.md) --- ### fast-subsample **Description:** Fast BAM subsampling using SMAI index with clustered I/O. Subsample reads | Property | Value | |----------|-------| | SKILL.md | `../skills/fast-subsample/SKILL.md` | # Fast BAM Subsample Fast, reproducible BAM subsampling using SMAI (SMA Index) virtual offset indexes with clustered I/O. [Full documentation](../skills/fast-subsample/SKILL.md) --- ### gene-coordinate-validator **Description:** Look up, validate, and cross-reference gene coordinates from NCBI, Ensembl, and UCSC before using them in any analysis. Prevents coordinate errors that silently corrupt downstream results (wrong BED tracks, empty VCFs, failed alignments). Use BEFORE any analysis that requires gene coordinates — especially for gene families, paralogs, pseudogenes, and pharmacogenes. Triggers on gene lookup, coordinate validation, gene position, GRCh38 coordinates, gene boundaries, annotation check, or when starting work on a new gene/locus. Also use when coordinates produce zero-alignment results or empty outputs, which often indicates wrong positions. | Property | Value | |----------|-------| | SKILL.md | `../skills/gene-coordinate-validator/SKILL.md` | # Gene Coordinate Validator [Full documentation](../skills/gene-coordinate-validator/SKILL.md) --- ### gg-pipeline **Description:** Run the full Golden Gate QC pipeline end-to-end. Chains gg extract → | Property | Value | |----------|-------| | SKILL.md | `../skills/gg-pipeline/SKILL.md` | # Golden Gate QC Pipeline Run the full GG QC pipeline from oligo inventory through IGV visualization reports. [Full documentation](../skills/gg-pipeline/SKILL.md) --- ### git-sync **Description:** Commit and push changes in sma-seq-workspace and smaseq-qc submodule | Property | Value | |----------|-------| | SKILL.md | `../skills/git-sync/SKILL.md` | # Git Sync Commit and push both the sma-seq-workspace and smaseq-qc submodule in the correct order. [Full documentation](../skills/git-sync/SKILL.md) --- ### golden-gate-assembly **Description:** Golden Gate cloning assembly design for combinatorial variant libraries. Use when designing oligo pools for star allele synthesis, mapping PharmVar haplotypes to template regions, analyzing multi-variant part requirements, identifying overhang conflicts, generating assembly instructions, or planning SMA-seq library construction. Triggers on requests involving Golden Gate assembly, Type IIS cloning, combinatorial cloning, star allele synthesis, PharmVar haplotype construction, BsaI/BsmBI assembly, or oligo pool design. | Property | Value | |----------|-------| | SKILL.md | `../skills/golden-gate-assembly/SKILL.md` | # Golden Gate Assembly Design Design combinatorial Golden Gate cloning assemblies for star allele synthesis and SMA-seq library construction. [Full documentation](../skills/golden-gate-assembly/SKILL.md) --- ### greatlakes-sync **Description:** Synchronize experiment data between Great Lakes HPC and local storage | Property | Value | |----------|-------| | SKILL.md | `../skills/greatlakes-sync/SKILL.md` | # Great Lakes Sync Automated experiment discovery on Great Lakes HPC with database synchronization and GitHub registry updates. [Full documentation](../skills/greatlakes-sync/SKILL.md) --- ### health-check **Description:** System health monitoring for ONT Ecosystem. Verifies Python environment, | Property | Value | |----------|-------| | SKILL.md | `../skills/health-check/SKILL.md` | # Health Check - System Diagnostics Comprehensive health monitoring and diagnostics for the ONT Ecosystem environment. [Full documentation](../skills/health-check/SKILL.md) --- ### igv-batch **Description:** Batch IGV report generation for multiple patients and gene regions. Use when generating IGV HTML reports across many patient × gene-region combinations from the experiment registry — e.g., before a clinical review session or panel-wide QC pass — instead of producing each report manually with /igv-report. | Property | Value | |----------|-------| | SKILL.md | `../skills/igv-batch/SKILL.md` | # IGV Batch Report Generation 1. Read the experiment registry to identify BAM files and gene regions 2. Validate BAM index files exist (.bai) 3. Generate igv-reports HTML for each patient/region combination 4. Use local /tmp for intermediate sorting, not network mounts 5. For HPC: use SLURM array jobs with verified account/partition 6. Watch for chrM coordinate overflow — clamp BED regions to reference length [Full documentation](../skills/igv-batch/SKILL.md) --- ### igv-report **Description:** Generate strand-specific IGV HTML reports with coordinate safety checks | Property | Value | |----------|-------| | SKILL.md | `../skills/igv-report/SKILL.md` | [Full documentation](../skills/igv-report/SKILL.md) --- ### ingest-transcripts **Description:** Ingest Tactiq meeting transcripts into the Athey Lab Wiki with status-check-first, incremental commits, and link verification. Use when there are pending Tactiq markdown exports that need filing into structured wiki pages, especially after a meeting batch. Use instead of lab-wiki-tactiq for reliable batch processing. Trigger on phrases like 'ingest transcripts', 'fill in transcript summaries', 'process meeting notes batch'. Enforces: (1) status check before any edit, (2) one commit per transcript, (3) link verification before each commit. | Property | Value | |----------|-------| | SKILL.md | `../skills/ingest-transcripts/SKILL.md` | # ingest-transcripts You are ingesting Tactiq meeting transcripts into the Athey Lab Wiki at `~/repos/lab-wiki/`. [Full documentation](../skills/ingest-transcripts/SKILL.md) --- ### lab-doctor **Description:** Comprehensive lab health check with a single 0-100 score. Aggregates CI status, workflow lint, refs drift, atom adoption, README freshness, experiment backlog, and stale clones into one number + a per-axis breakdown. Use when the user asks "how healthy is the lab", "lab health check", "audit", or wants a one-line answer to "is everything ok?". Distinct from /lab-status (data dashboard) and /lab-fixall (cleanup runner) — this is just diagnosis. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-doctor/SKILL.md` | # /lab-doctor — comprehensive lab health check [Full documentation](../skills/lab-doctor/SKILL.md) --- ### lab-drive **Description:** Search and mine the lab Google Drive corpus (via rclone gdrive remote) for lab-relevant content — proposals, manuscripts in progress, literature PDFs, slide decks, thesis drafts. Extracts DOIs from PDFs to feed into refs/master.bib; exposes filename search; builds a prose index for reuse. Use when user asks to "find that old proposal", "search Drive for X", "mine refs from my literature folder", or to pull prior prose for a new manuscript section. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-drive/SKILL.md` | # lab-drive Fast, read-only access to the lab Google Drive via the `gdrive:` rclone remote (already configured as `drive.readonly`). Four operations: 1. **Search** — filename / extension / folder filter across the whole Drive 2. **Fetch** — download a specific file on demand 3. **PDF-DOI mine** — enumerate PDFs in a folder, extract DOIs from each 4. **Prose index** — build a SQLite index of doc contents for grep / reuse [Full documentation](../skills/lab-drive/SKILL.md) --- ### lab-fixall **Description:** End-of-session lab-wide cleanup sweep. Refreshes canonical READMEs across every active paper, validates atom schemas, runs ruff --fix on lab-papers + lab-system, regenerates lab-wiki papers.html if stale, and reports on any uncommitted changes that need user review. Use when the user says "fix everything", "lab cleanup", "end of session sweep", or "tidy up the lab". Distinct from /consolidate (which is for archiving + canonical-skill sync); this is for catching the small drift items. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-fixall/SKILL.md` | # /lab-fixall — end-of-session lab cleanup sweep [Full documentation](../skills/lab-fixall/SKILL.md) --- ### lab-inbox **Description:** Mine Gmail (gregfar@umich.edu) for paper-relevant intelligence — proposed citations, submission status changes, "For editing" drafts from Athey, funding opportunities, GitHub CI failures. Writes structured outputs to ~/.lab-papers/inbox/ consumable by the morning brief and dashboard. Use when user asks "what's in my email about X paper", "any new funding opportunities", "did Brian send edits", or on a scheduled agentic run. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-inbox/SKILL.md` | # lab-inbox Turns Gmail into structured, paper-linked lab intelligence. Works in two modes: - **Manual**: user asks a question → skill runs the appropriate scanner. - **Scheduled** (via the `/schedule` plugin): a Claude agent runs the full scan suite hourly or daily and writes findings to `~/.lab-papers/inbox/*.md`. The existing `wiki_watcher.py` regenerates the dashboard on its next tick, so findings land on the live site within minutes. [Full documentation](../skills/lab-inbox/SKILL.md) --- ### lab-manuscript **Description:** Build, check, and maintain any lab manuscript registered in lab-papers/papers.yaml. Generalizes the sma-manuscript and endreason-manuscript skills. Use when the user asks to build, compile, lint, regenerate figures, refresh references, or check status for a specific paper. Takes --paper . | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-manuscript/SKILL.md` | # lab-manuscript Single entry point for working on **any** lab manuscript. Reads `~/repos/lab-papers/papers.yaml` for paper metadata, dispatches to the right build command, refs refresh, figure regeneration, or submission check. [Full documentation](../skills/lab-manuscript/SKILL.md) --- ### lab-paper-status **Description:** Cross-paper status dashboard for all lab manuscripts. Reads papers.yaml, introspects each paper's directory, and renders an HTML dashboard showing word counts, figure counts, TODO markers, last build status, and target dates side-by-side. Use when the user asks "how are all our papers doing?", "what's the status of our manuscripts?", or wants a lab meeting update. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-paper-status/SKILL.md` | # lab-paper-status Renders a single HTML page summarising every paper in `papers.yaml` so the lab PI / advisor can see all five concurrent manuscripts at a glance. [Full documentation](../skills/lab-paper-status/SKILL.md) --- ### lab-papers-bump **Description:** Propose lab-render.yml SHA-pin updates as PRs across all paper + project consumer repos discovered via lab-papers/papers.yaml. Triggers on phrases like "bump lab-render", "update render pin", "propagate lab-papers main", "ship lab-papers main to consumers". | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-papers-bump/SKILL.md` | # lab-papers-bump Walks every consumer repo (paper or project with a `github_repo:` set in `papers.yaml`), updates its `.github/workflows/build.yml` SHA pin to the latest lab-papers main commit, and opens a PR per repo. User reviews + merges per repo. Drift becomes **visible** (PRs accumulate) instead of catastrophic (all-red simultaneously). [Full documentation](../skills/lab-papers-bump/SKILL.md) --- ### lab-query **Description:** Query the lab knowledge index — search across lab-wiki, lab-papers inbox, refs, and papers.yaml. Returns answers with citations. Use when the user asks a natural-language knowledge question whose answer might live in lab notes, transcripts, papers inbox, or the citation library. Triggers on phrases like "what do we know about", "find that decision", "search the wiki for", "what's in the inbox about". Calls the local lab-query backend on localhost:7861. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-query/SKILL.md` | # lab-query You are routing a question to the lab's local query index. [Full documentation](../skills/lab-query/SKILL.md) --- ### lab-refs **Description:** Agent-driven curator for the lab reference library. Use when the user asks to find duplicate refs, suggest citations for a draft paragraph, fill in missing DOIs, clean up the library, or audit citation hygiene. Complements the lab-refs CLI — this skill adds natural-language reasoning on top of deterministic validation. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-refs/SKILL.md` | # lab-refs Natural-language curator for `lab-papers/refs/master.bib`. The CLI (`python -m refs.bin.lab_refs ...`) provides deterministic validation; this skill layers agent reasoning on top for tasks that require judgement. [Full documentation](../skills/lab-refs/SKILL.md) --- ### lab-site-template **Description:** Generate a consistent GitHub Pages landing page for any lab paper or project repo. Renders docs/landing.html, docs/landing.css, and .github/workflows/pages.yml. Auto-detects paper vs project by cross-referencing ~/repos/lab-papers/papers.yaml. Use when rolling out a new repo's public face, refreshing an existing landing, or regenerating after repo metadata changes. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-site-template/SKILL.md` | # lab-site-template Generates a uniform landing page for any lab repo — paper or project — with a Stripe-lite visual design matching the `fragment-viewer` reference site. [Full documentation](../skills/lab-site-template/SKILL.md) --- ### lab-status **Description:** Show a single-screen lab dashboard — atom adoption + README freshness across every paper, open PRs, refs.bib drift vs lab citation library, latest CI status per repo, days-to-deadline per paper, stale clones. Use when the user asks "what's the state of the lab", "lab dashboard", "lab status", "what's going on across all papers", or wants a session-start orientation. Powered by the menu skill's gather_context.py --lab-status. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-status/SKILL.md` | # /lab-status — single-screen lab dashboard [Full documentation](../skills/lab-status/SKILL.md) --- ### lab-submission-check **Description:** Journal-aware pre-submission checklist for any lab manuscript. Validates word counts, figure count limits, reference format, required sections, file format, and submission metadata against the target journal's rules. Use before submitting to Nature Genetics, Clinical Pharmacology & Therapeutics, Scientific Data, or other supported journals. Generalizes the check-submission skill. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-submission-check/SKILL.md` | # lab-submission-check Runs the target journal's submission checklist against a manuscript. Journal rules live in `skills/lab-submission-check/journals/.yaml`. [Full documentation](../skills/lab-submission-check/SKILL.md) --- ### lab-textbook-search **Description:** | | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-textbook-search/SKILL.md` | # /lab-textbook-search — query the textbook + lab corpus from anywhere [Full documentation](../skills/lab-textbook-search/SKILL.md) --- ### lab-transcripts **Description:** Paper-centric view of the Athey Lab wiki's meeting and decision corpus. Answers "what meetings were about the SMAseq paper?", "what decisions affect the PGx paper?", "which papers were discussed last week?". Does NOT ingest or parse raw transcripts — that's the lab-wiki-tactiq skill's job. Use when the user asks paper-first questions about lab activity. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-transcripts/SKILL.md` | # lab-transcripts **Paper-centric lens over lab-wiki's structured knowledge.** This skill does not touch raw Google Drive transcripts; it reads what `lab-wiki-tactiq` has already produced and projects it through the paper IDs in `lab-papers/papers.yaml`. [Full documentation](../skills/lab-transcripts/SKILL.md) --- ### lab-wiki **Description:** Operate the Athey Lab Wiki — ingest sources into structured pages, query the wiki, run health lint. ALWAYS read AGENTS.md at ~/repos/lab-wiki/AGENTS.md before any operation. Use when the user asks to "ingest", "file", "add to wiki", "query the wiki", "lint the wiki", or references a paper/experiment that should be filed. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-wiki/SKILL.md` | # lab-wiki You are about to operate the **Athey Lab Wiki** at `~/repos/lab-wiki/`. This is the lab's compounding knowledge base — markdown files, cross-referenced, LLM-maintained. [Full documentation](../skills/lab-wiki/SKILL.md) --- ### lab-wiki-calendar **Description:** Pre-create wiki transcript pages from upcoming Google Calendar events so transcripts merge in rather than creating new pages. Use when the user says "prep upcoming meetings", "calendar sync", "generate meeting pages", or when a scheduled cron triggers weekly calendar prep. Fetches events via Google Calendar MCP, classifies them, and writes scheduled-status pages to transcripts/. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-wiki-calendar/SKILL.md` | # lab-wiki-calendar You are pre-generating meeting pages in the Athey Lab Wiki at `~/repos/lab-wiki/` (real path: `/mnt/d/lab-wiki/`) from upcoming Google Calendar events. [Full documentation](../skills/lab-wiki-calendar/SKILL.md) --- ### lab-wiki-tactiq **Description:** Ingest Tactiq meeting transcripts from Google Drive into the lab-wiki. Reads raw markdown exports, writes structured meeting pages with summary/decisions/action items, walks cross-references to projects/entities/people, and promotes lab-wide decisions to the decisions/ directory. Use when the user says "ingest transcripts", "process meeting notes", "tactiq sync", or when a scheduled cron triggers transcript processing. | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-wiki-tactiq/SKILL.md` | # lab-wiki-tactiq You are processing Tactiq-exported meeting transcripts into the Athey Lab Wiki at `~/repos/lab-wiki/` (real path: `/mnt/d/lab-wiki/`). [Full documentation](../skills/lab-wiki-tactiq/SKILL.md) --- ### lab-workspace **Description:** Activate, pin, inspect, and health-check workspaces (projects + papers) from the lab-system registry. Use when the user says "/lab-workspace", "what workspace am I in", "activate ", "pin this workspace", "unpin", "what''s active", "doctor my workspace", or seems to be setting up a session to work on a specific project/paper. Six subcommands — status, activate, off, detect, resolve, doctor. Requires lab-system installed (ships M0 registry + M1 activation). | Property | Value | |----------|-------| | SKILL.md | `../skills/lab-workspace/SKILL.md` | # /lab-workspace — workspace activation + inspection [Full documentation](../skills/lab-workspace/SKILL.md) --- ### library-prep-comparison **Description:** Compare different SMA-seq library preparation methods (e.g., no_trim | Property | Value | |----------|-------| | SKILL.md | `../skills/library-prep-comparison/SKILL.md` | # Library Prep Comparison Skill Compare different SMA-seq library preparation methods with comprehensive statistical analysis, per-barcode Q-score and error rate comparisons, orientation-dependent effects, and publication figures. [Full documentation](../skills/library-prep-comparison/SKILL.md) --- ### lifecycle **Description:** Experiment lifecycle tracking and pipeline orchestration | Property | Value | |----------|-------| | SKILL.md | `../skills/lifecycle/SKILL.md` | # Lifecycle - Pipeline Orchestration and Tracking Experiment lifecycle tracking and pipeline orchestration skill. Wraps the `ont_lifecycle.py` CLI for managing experiment progress through defined pipeline stages. [Full documentation](../skills/lifecycle/SKILL.md) --- ### link-health-monitor **Description:** Continuous link-health monitor across lab repos. Checks daily, auto-opens issues on persistent failures, renders dashboard. Use when checking badge/link drift. | Property | Value | |----------|-------| | Pipeline Stage | `infrastructure` | | SKILL.md | `../skills/link-health-monitor/SKILL.md` | # Link Health Monitor Walks every active (non-archived) repo in the lab GitHub org, scrapes every README link + shields.io badge URL, probes each appropriately, and publishes a daily dashboard + opens/closes GitHub issues when links go bad or recover. [Full documentation](../skills/link-health-monitor/SKILL.md) --- ### locus-igv-builder **Description:** Build comprehensive IGV sessions for any complex genomic locus. Generates | Property | Value | |----------|-------| | SKILL.md | `../skills/locus-igv-builder/SKILL.md` | > **Prerequisite:** Run `/gene-coordinate-validator` to verify gene coordinates before using this skill. Wrong coordinates silently corrupt all downstream outputs. # Locus IGV Builder Generate all components needed for a comprehensive IGV visualization of any complex genomic locus: reference FASTA, annotation tracks, session XML, and interactive HTML maps. [Full documentation](../skills/locus-igv-builder/SKILL.md) --- ### manuscript **Description:** Generate publication-quality figures and tables from ONT sequencing experiments. | Property | Value | |----------|-------| | SKILL.md | `../skills/manuscript/SKILL.md` | # Manuscript Skill Generate publication-quality figures and tables from ONT sequencing experiments. [Full documentation](../skills/manuscript/SKILL.md) --- ### manuscript-status **Description:** Show SMA-seq manuscript completion status — word counts, figure status, markers, sources. Use when checking SMA-seq Nature Genetics manuscript progress — section word counts, figure-stub completion, TODO markers, and last-touched timestamps for source files — typically before a writing session or status update. | Property | Value | |----------|-------| | SKILL.md | `../skills/manuscript-status/SKILL.md` | # Manuscript Status Dashboard Show comprehensive status of the SMA-seq Nature Genetics manuscript. [Full documentation](../skills/manuscript-status/SKILL.md) --- ### menu **Description:** Interactive menu walker that shows all lab functionality as clickable options with context-aware suggestions. Use when the user asks "what can I do", "menu", "show me options", "help me pick", "what should I work on", "propose next steps", or seems unsure of direction. Gathers recent context (meetings, experiments, commits, handoffs, stale items) + local context (cwd, workspace.yaml sidecar, .project/ tree, nearby CLAUDE.md). Drills from broad category → specific actions → execution, always offering a custom-input escape hatch at every level. | Property | Value | |----------|-------| | SKILL.md | `../skills/menu/SKILL.md` | # /menu — interactive lab functionality walker [Full documentation](../skills/menu/SKILL.md) --- ### morning **Description:** Session-start orientation. Runs the lab-status text dashboard (deadlines + CI + experiments + PRs + paper inventory) and surfaces ONE concrete top-priority action. Use at the start of a session, when the user says "good morning", "what's the lab look like", "session start", or "where do I start". Distinct from /menu (navigable launcher) and /lab-status (full dashboard) — this is the one-glance + one-action variant. | Property | Value | |----------|-------| | SKILL.md | `../skills/morning/SKILL.md` | # /morning — session-start orientation [Full documentation](../skills/morning/SKILL.md) --- ### multi-locus-enrichment **Description:** >- | Property | Value | |----------|-------| | SKILL.md | `../skills/multi-locus-enrichment/SKILL.md` | # Multi-Locus Enrichment Characterization After detecting enriched loci (via `/cas9-enrichment` or similar), this skill runs deeper characterization at every target: variants, methylation, depth, and structural variants. It produces one unified report covering all loci. [Full documentation](../skills/multi-locus-enrichment/SKILL.md) --- ### onboard-member **Description:** Generate a complete Athey Lab onboarding bundle for a new member (pre-approved Volunteer Services placement form, general onboarding doc, initial email, lab-wide welcome email, and lab-wiki person-page stub) from a single YAML config. Handles volunteer / UROP / paid / graduate role types and wet / dry / both tracks. Use when onboarding any new lab member, or when regenerating their bundle after a project reassignment. | Property | Value | |----------|-------| | SKILL.md | `../skills/onboard-member/SKILL.md` | # onboard-member Automates the first-48-hours onboarding artifacts the Athey Lab produces by hand every time a new member joins. Reads one YAML config; writes five rendered files ready to convert, send, and commit. [Full documentation](../skills/onboard-member/SKILL.md) --- ### ont-align **Description:** Oxford Nanopore alignment with minimap2/dorado, reference genome management, | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-align/SKILL.md` | # ONT Align - Alignment & Edit Distance Alignment toolkit for Oxford Nanopore data with reference management, QC, and sequence comparison. [Full documentation](../skills/ont-align/SKILL.md) --- ### ont-experiments-v2 **Description:** Enhanced Oxford Nanopore experiment management with event-sourced registry, | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-experiments-v2/SKILL.md` | # ONT Experiments v2 - Enhanced Registry Foundational tool for discovering, tracking, and orchestrating Oxford Nanopore sequencing experiments with improved pipeline integration. [Full documentation](../skills/ont-experiments-v2/SKILL.md) --- ### ont-explorer **Description:** Comprehensive experiment exploration - metadata collection, visualization, | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-explorer/SKILL.md` | # ONT Experiment Explorer Comprehensive tool for exploring Oxford Nanopore experiments. Collects metadata, generates visualizations, and suggests analysis scripts with detailed descriptions. [Full documentation](../skills/ont-explorer/SKILL.md) --- ### ont-lifecycle **Description:** Experiment lifecycle tracking with dependency graphs, stage progression, | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-lifecycle/SKILL.md` | # ONT Lifecycle - Experiment Pipeline Tracking Comprehensive pipeline status and lifecycle tracking system for ONT experiments. Provides visibility into experiment progress through a CLI command and web dashboard, with full Claude Code UI integration. [Full documentation](../skills/ont-lifecycle/SKILL.md) --- ### ont-metadata **Description:** Extract and manage metadata from Oxford Nanopore sequencing experiments | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-metadata/SKILL.md` | # ONT Metadata Parser Extract run-level metadata from Oxford Nanopore POD5 and Fast5 raw data files without requiring `final_summary.txt` files. [Full documentation](../skills/ont-metadata/SKILL.md) --- ### ont-monitor **Description:** Real-time and retrospective Oxford Nanopore sequencing run monitoring. | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-monitor/SKILL.md` | # ONT Monitor - Sequencing Run Monitoring Monitor Oxford Nanopore sequencing runs in real-time or analyze completed runs retrospectively. ## Integration with ont-experiments This skill uses **Pattern B orchestration**: ```bash # Recommended: Run through ont-experiments for full provenance tracking ont_experiments.py run monitoring exp-abc123 --live ont_experiments.py run monitoring exp-abc123 --json report.json --plot metrics.png # Direct execution (no registry event logging) python3 ont_monitor.py /path/to/run --live ``` When run through `ont_experiments.py run`, automatically captures: - Full command with parameters - Output file checksums - Duration and exit code - HPC metadata (SLURM job ID, nodes) - Results summary in registry [Full documentation](../skills/ont-monitor/SKILL.md) --- ### ont-pipeline **Description:** Oxford Nanopore multi-step workflow orchestration with unified QC aggregation. | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-pipeline/SKILL.md` | # ONT Pipeline - Workflow Orchestration Multi-step analysis pipeline orchestrator with unified QC aggregation and pharmacogenomics support. [Full documentation](../skills/ont-pipeline/SKILL.md) --- ### ont-public-data **Description:** Discover, stream, and analyze public ONT datasets from S3 without full | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-public-data/SKILL.md` | # ONT Public Data Hub Discover, download, and compare public Oxford Nanopore datasets from SRA/ENA. Search public databases, organize datasets with bookmarks and collections, and compare local experiments against public references. [Full documentation](../skills/ont-public-data/SKILL.md) --- ### ont-welcome **Description:** Session start welcome with context-aware suggestions. Presents ecosystem | Property | Value | |----------|-------| | SKILL.md | `../skills/ont-welcome/SKILL.md` | # ONT Welcome Session start skill that presents ecosystem status and offers context-aware actions. Designed to be invoked automatically at session start or manually via `/ont-welcome`. [Full documentation](../skills/ont-welcome/SKILL.md) --- ### overnight-ingest **Description:** Automated overnight maintenance for the Athey Lab Wiki — syncs Tactiq transcripts from Google Drive via rclone, ingests new meetings through the tactiq pipeline, fills skeleton summaries with structured meeting notes, refreshes the lab-system entity catalog and themes, and commits changes locally. Use when the user says "run overnight ingest", "nightly maintenance", "sync and ingest transcripts", "overnight wiki refresh", or when triggered as a scheduled task. Also use for manual catch-up runs during the day. | Property | Value | |----------|-------| | SKILL.md | `../skills/overnight-ingest/SKILL.md` | # overnight-ingest You are running the Athey Lab Wiki overnight maintenance pipeline on Greg's Windows workstation. The wiki lives at `D:\lab-wiki` (WSL: `/mnt/d/lab-wiki/`). This skill orchestrates 6 stages that sync, ingest, enrich, and commit wiki content. It is designed to run unattended (scheduled task, no user present) but can also be invoked manually. [Full documentation](../skills/overnight-ingest/SKILL.md) --- ### pacbio-igv-reports **Description:** Generate standalone HTML IGV reports from PacBio HiFi or ONT long-read | Property | Value | |----------|-------| | SKILL.md | `../skills/pacbio-igv-reports/SKILL.md` | # PacBio / Long-Read IGV Reports Generate standalone HTML IGV reports from PacBio HiFi or ONT long-read sequencing data. Each report embeds aligned reads in an interactive igv.js viewer that opens in any browser -- no IGV desktop required. [Full documentation](../skills/pacbio-igv-reports/SKILL.md) --- ### pacbio-qscore **Description:** Per-library Q-score distribution, calibration, and error-rate analysis | Property | Value | |----------|-------| | SKILL.md | `../skills/pacbio-qscore/SKILL.md` | # PacBio HiFi Q-score Analysis A PacBio-native Q-score analyzer for cohorts of HiFi BAMs (typically produced by `pbmm2 map-hifi`). Complements `/qscore-calibration` (which is ONT-shaped and needs a `sequencing_summary.txt`). [Full documentation](../skills/pacbio-qscore/SKILL.md) --- ### paralog-discriminator **Description:** Discriminate reads between high-identity paralogs/pseudogenes by identifying | Property | Value | |----------|-------| | SKILL.md | `../skills/paralog-discriminator/SKILL.md` | > **Prerequisite:** Run `/gene-coordinate-validator` to verify gene coordinates before using this skill. Wrong coordinates silently corrupt all downstream outputs. # Paralog Discriminator Identify diagnostic sequence differences between high-identity gene family members and generate IGV-ready variant tracks to detect mismapped reads. [Full documentation](../skills/paralog-discriminator/SKILL.md) --- ### pharmvar-genotype **Description:** Pharmacogenomic star allele genotyping using PharmVar haplotype definitions | Property | Value | |----------|-------| | SKILL.md | `../skills/pharmvar-genotype/SKILL.md` | > **CRITICAL PREREQUISITE:** BAMs MUST be aligned to a **primary-only reference** (no ALT contigs). GRCh38 with ALT haplotype contigs (HSCHR*) steals reads from CYP2D6, causing false negatives. Use `/alt-contig-rescue` or filter with `samtools view -F 0x900` before genotyping. # PharmVar Star Allele Genotyping (v2) Call pharmacogene variants from long-read BAMs, match to PharmVar star allele definitions, assign diplotypes, estimate copy number, and predict metabolizer phenotypes. [Full documentation](../skills/pharmvar-genotype/SKILL.md) --- ### pipeline **Description:** SMA-seq MMID pipeline library providing modular L0-L6 layers for data | Property | Value | |----------|-------| | SKILL.md | `../skills/pipeline/SKILL.md` | # Pipeline - SMA-seq MMID Layers Modular Python library implementing the MMID (Measurement, Modeling, Improvement, Deploy) pipeline layers for SMA-seq analysis. [Full documentation](../skills/pipeline/SKILL.md) --- ### pipeline-run **Description:** Run the full SMA-seq analysis pipeline on one or more experiments. Orchestrates | Property | Value | |----------|-------| | SKILL.md | `../skills/pipeline-run/SKILL.md` | # SMA-seq Pipeline Runner Run the standard analysis pipeline on experiments. Steps execute sequentially — each depends on the previous. [Full documentation](../skills/pipeline-run/SKILL.md) --- ### pipeline-status **Description:** Check SMA-seq pipeline completion status across all experiments. Shows which stages (merge, tag, align, classify, QC) are done, stale, or missing for each experiment. Use when wanting an at-a-glance summary of which experiments are stuck at which pipeline stage — for instance before an HPC sync, or when triaging which experiments need a re-run after a config change. | Property | Value | |----------|-------| | SKILL.md | `../skills/pipeline-status/SKILL.md` | # Pipeline Status Check the completion status of the SMA-seq analysis pipeline across all experiments. [Full documentation](../skills/pipeline-status/SKILL.md) --- ### plan-reconciler **Description:** Detect and optionally flip stale checkboxes in superpowers implementation plans. Use when the user says "/plan-reconciler", "reconcile plans", "any plans that finished but not checked off", "check plan status", or when /consolidate / /menu shows plans with suspicious done-but-unchecked state. Correlates each `- [ ]` step with file existence + recent git commits in the plan's repo; scores evidence; reports LIKELY_DONE candidates and can bulk-flip them on --apply. Report-first by design — never writes without the flag. | Property | Value | |----------|-------| | SKILL.md | `../skills/plan-reconciler/SKILL.md` | # /plan-reconciler — stale-checkbox auditor for superpowers plans [Full documentation](../skills/plan-reconciler/SKILL.md) --- ### plugin-doctor **Description:** Health-check and auto-fix for Claude Code plugins, skills, and hooks. Detects broken plugins, stale skills, hook failures, and known failure modes. | Property | Value | |----------|-------| | SKILL.md | `../skills/plugin-doctor/SKILL.md` | # Plugin Doctor Autonomous health-check and repair system for the Claude Code workspace. [Full documentation](../skills/plugin-doctor/SKILL.md) --- ### project-walkthrough **Description:** Interactive content-first questionnaire walkthrough for a lab project. Reads questions.yaml + answers.yaml from a project's .project/questionnaire/ directory, renders each unanswered question via AskUserQuestion, persists answers. Iterates in tier order (content → monitoring → maturity → identity) with a manual-unlock gate before identity-tier. Use when user says "walk me through project ", "start the walkthrough for ", or picks a walkthrough-ready project from /menu. | Property | Value | |----------|-------| | SKILL.md | `../skills/project-walkthrough/SKILL.md` | # /project-walkthrough — content-first project questionnaire walkthrough [Full documentation](../skills/project-walkthrough/SKILL.md) --- ### propose **Description:** Scan the full SMA-seq workspace and propose prioritized analyses, processing, | Property | Value | |----------|-------| | SKILL.md | `../skills/propose/SKILL.md` | # Propose - Intelligent Analysis Advisor Scans all available context across the SMA-seq workspace and proposes prioritized, actionable analyses. Covers experiment registries, output completeness, skill availability, cross-experiment comparisons, and manuscript readiness. [Full documentation](../skills/propose/SKILL.md) --- ### pypgx **Description:** PyPGx pharmacogenomic genotyping wrapper. Runs the long-read or NGS pipeline against the lab's CYP2D6/PGx panel (375 genes), pre-computes depth-of-coverage archives, manages per-gene control statistics, and batches multi-gene/multi-sample loops with consistent GRCh38 + PGx_v1.0.bed conventions. Use when running pypgx genotyping on Oxford Nanopore or Illumina BAMs, especially against CYP2D6 / CYP2D7 / CYP2D8 or the full pharmacogene panel. | Property | Value | |----------|-------| | SKILL.md | `../skills/pypgx/SKILL.md` | # pypgx Wrapper around `pypgx` (https://pypgx.readthedocs.io) — automated pharmacogenomic genotyping with copy-number prediction + diplotype calling. Covers the two-stage workflow Greg uses across the PGx adaptive-sampling paper: ``` BAM ──┬──> prepare-depth-of-coverage ──┐ ├──> create-input-vcf ───────────┼──> run-long-read-pipeline ──> diplotype + plots └──> compute-control-statistics ─┘ ``` [Full documentation](../skills/pypgx/SKILL.md) --- ### qc-advisor **Description:** AI-powered QC analysis for Oxford Nanopore sequencing. Provides troubleshooting | Property | Value | |----------|-------| | SKILL.md | `../skills/qc-advisor/SKILL.md` | # QC Advisor - AI-Powered QC Recommendations Analyzes Oxford Nanopore QC results and provides intelligent, actionable recommendations for troubleshooting, optimization, and next steps based on historical baselines and pattern detection. [Full documentation](../skills/qc-advisor/SKILL.md) --- ### qscore-calibration **Description:** Comprehensive Q-score calibration and discriminability analysis for Oxford | Property | Value | |----------|-------| | SKILL.md | `../skills/qscore-calibration/SKILL.md` | # Q-Score Calibration Analysis Comprehensive Q-score calibration and discriminability analysis for Oxford Nanopore sequencing data. [Full documentation](../skills/qscore-calibration/SKILL.md) --- ### reflect **Description:** Process queued learnings and apply them to CLAUDE.md. Captures user corrections | Property | Value | |----------|-------| | SKILL.md | `../skills/reflect/SKILL.md` | # Reflect: Learning Memory System Process user corrections and preferences captured during sessions, applying them to CLAUDE.md for persistent memory across conversations. [Full documentation](../skills/reflect/SKILL.md) --- ### registry-browser **Description:** Interactive HTML browser for the ONT experiment registry with filtering, | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-browser/SKILL.md` | # Registry Browser Skill v3.0 Comprehensive registry management with validation, re-analysis capabilities, and completeness tracking. Integrates with 42basepairs.com for visual S3 browsing. [Full documentation](../skills/registry-browser/SKILL.md) --- ### registry-explorer **Description:** Explore and search the ONT experiment registry with advanced filtering | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-explorer/SKILL.md` | # Registry Explorer Skill Deep inspection of source data files to extract comprehensive metadata for ONT experiments. [Full documentation](../skills/registry-explorer/SKILL.md) --- ### registry-scrutinize **Description:** Audit, validate, and fix ONT experiment registry entries with comprehensive | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-scrutinize/SKILL.md` | # Registry Scrutinize Skill v1.0 Deep validation and enrichment system for ONT experiment registry entries. [Full documentation](../skills/registry-scrutinize/SKILL.md) --- ### registry-server **Description:** Flask API server for federated experiment tracking with multi-location | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-server/SKILL.md` | # Registry Server Skill REST API server for the federated experiment tracking system. Enables agents at different locations (sequencers, HPCs, cloud) to report experiments and query the central registry. [Full documentation](../skills/registry-server/SKILL.md) --- ### registry-unified **Description:** Build a single sortable/filterable HTML view of all lab experiments across ONT + SMA registries. Self-contained output — no network deps, works offline. | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-unified/SKILL.md` | # Registry Unified View Generates a single HTML page listing **every experiment across all lab registries** (ONT + SMA) with client-side sort, filter, and source-chip toggle. Distinct from `/registry-browser` (ONT-only) and `/ont-explorer` (per-experiment deep dive). [Full documentation](../skills/registry-unified/SKILL.md) --- ### registry-validator **Description:** Validate SMA registry referential integrity across all 6 sub-registries. Checks foreign keys, orphaned records, target checksums, and experiment completeness. Use when the SMA registry has been edited manually or via bulk import, before pushing registry changes, or when investigating why a downstream skill complains about missing registry references. | Property | Value | |----------|-------| | SKILL.md | `../skills/registry-validator/SKILL.md` | # Registry Validator Validate the SMA registry database for referential integrity, orphaned records, and data consistency. [Full documentation](../skills/registry-validator/SKILL.md) --- ### repeat-expansion-analyzer **Description:** Size trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide | Property | Value | |----------|-------| | SKILL.md | `../skills/repeat-expansion-analyzer/SKILL.md` | # Repeat Expansion Analyzer Sizes short tandem repeat (STR) expansions from long-read sequencing data (PacBio HiFi or ONT) at known disease loci. Designed for Cas9/PureTarget enrichment panels but works with any aligned long reads. [Full documentation](../skills/repeat-expansion-analyzer/SKILL.md) --- ### repo-analyzer **Description:** Analyze lab paper/project repositories for gaps, completeness, and recommendations. Use when auditing repository structure, identifying missing components, recommending next steps for repo development, or comparing repo maturity across the lab. | Property | Value | |----------|-------| | SKILL.md | `../skills/repo-analyzer/SKILL.md` | # Repo Analyzer Analyzes lab paper and project repositories to identify structural gaps, generate actionable recommendations, and provide peer comparison suggestions. [Full documentation](../skills/repo-analyzer/SKILL.md) --- ### seed-project-ledgers **Description:** Step through lab projects one at a time, bootstrapping each project''s provenance ledger + running its first reflection report. Use when the user asks to "seed project ledgers", "bootstrap reflection for new projects", "iterate through projects", or wants a loop/scheduled task to process un-seeded project shells. Tracks progress in `~/.cache/lab-seed-project-ledgers/progress.json` so repeated invocations advance one project at a time. Safe: commits locally inside each project''s repo; NEVER pushes, NEVER merges, NEVER creates PRs — those remain operator-driven per the shell-vs-code-home + user-drives-init rules. | Property | Value | |----------|-------| | SKILL.md | `../skills/seed-project-ledgers/SKILL.md` | # /seed-project-ledgers Processes **one** lab project per invocation. **Pass 1 (seed):** zero-ledger projects get `make bootstrap` + `make reflect`. **Pass 2 (refresh):** once every eligible project has been seeded, the skill rotates through the skill-seeded set (NOT pre-existing mature projects) in oldest-touched order, running `make reflect` again so scheduled `/loop` ticks keep producing useful output. `--min-age ` (default 3600) skips recently-touched projects to prevent thrashing. Commits land locally inside each project's repo. After each invocation the user reviews the diff, accepts or reverts, then invokes again (or leaves `/loop` to auto-pace). [Full documentation](../skills/seed-project-ledgers/SKILL.md) --- ### skill-doctor **Description:** Tier-1 health auditor for the lab's 84-skill ecosystem. Lints SKILL.md frontmatter, detects broken symlinks in ~/.claude/skills/, finds divergence between ont-ecosystem and ont-ecosystem-test mirrors, flags stale skills (>90d), missing-test coverage, skills that exist locally but aren't backed in any git repo, and external cron/timer heartbeats (e.g. the nightly dashboard snapshot). Runs every 30 min via cron; outputs JSON + markdown to ~/.lab-skills/. Use when the user asks "how healthy is the skill ecosystem", "which skills are broken", or "audit my skills". | Property | Value | |----------|-------| | SKILL.md | `../skills/skill-doctor/SKILL.md` | # skill-doctor Read-only health auditor for every Claude skill the lab has authored. Complements `consolidate` (which fixes drift) by being a fast, deterministic *detector* — produces a punch list that downstream tools (`consolidate`, `skill-recommender`, PR CI, GitHub Issues) consume. [Full documentation](../skills/skill-doctor/SKILL.md) --- ### skill-maker **Description:** Create, update, and manage Claude skills automatically. Use when developing | Property | Value | |----------|-------| | SKILL.md | `../skills/skill-maker/SKILL.md` | # Skill Maker Automates the creation, updating, and distribution of Claude skills across all platforms. [Full documentation](../skills/skill-maker/SKILL.md) --- ### skill-orchestration **Description:** Intelligent skill routing for ONT Ecosystem. Finds the right skill for | Property | Value | |----------|-------| | SKILL.md | `../skills/skill-orchestration/SKILL.md` | # Skill Orchestration - Intelligent Skill Routing Automatically routes requests to appropriate ONT Ecosystem skills based on context analysis, skill availability, and trigger evaluation. [Full documentation](../skills/skill-orchestration/SKILL.md) --- ### skill-recommender **Description:** Tier-2 agentic auditor for the lab's skill ecosystem. Reads shell history, lab-papers/inbox state, lab-wiki recent activity, and skill-doctor's health.json to propose (a) new skills for repeated workflows, (b) deprecation candidates for never-invoked skills, (c) merge candidates when 2 skills overlap, (d) test-coverage targets. Runs daily via cron; output to ~/.lab-skills/proposals.md for human review. Use when the user asks "what skills should I create", "which skills are unused", or "review my skill ecosystem". | Property | Value | |----------|-------| | SKILL.md | `../skills/skill-recommender/SKILL.md` | # skill-recommender Daily agentic review of the lab's skill landscape. Where `skill-doctor` reports *what is broken*, this skill reports *what should change* — new skills to build, old ones to retire, pairs to merge, untested ones to fix. [Full documentation](../skills/skill-recommender/SKILL.md) --- ### sma-analysis **Description:** SMA-seq multi-experiment alignment-based classification and visualization | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-analysis/SKILL.md` | # SMA-seq Analysis Pipeline Multi-experiment analysis with two-stage alignment classification, demux evaluation, and publication-quality visualization. [Full documentation](../skills/sma-analysis/SKILL.md) --- ### sma-igv-reports **Description:** Generate standalone HTML IGV reports for SMA-seq experiments. Fast-subsamples | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-igv-reports/SKILL.md` | # SMA-seq IGV Reports Generate standalone HTML IGV reports for SMA-seq experiments. Each report embeds aligned reads in an interactive igv.js viewer that opens in any browser — no IGV desktop required. [Full documentation](../skills/sma-igv-reports/SKILL.md) --- ### sma-launcher **Description:** Discover and run SMA-seq analysis tools. Use when the user describes an analysis task and you need to find the right script. | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-launcher/SKILL.md` | # SMA Launcher Find the right tool for any SMA-seq analysis task. Run `sma_launcher.py` for interactive use, or recommend tools directly from the registry below. [Full documentation](../skills/sma-launcher/SKILL.md) --- ### sma-pipeline **Description:** Full SMA-seq pipeline orchestrator with database initialization, POD5 | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-pipeline/SKILL.md` | # SMA Pipeline - Single-Molecule-Accuracy Analysis Full SMA-seq analysis pipeline with database initialization, POD5 metadata extraction, BAM tagging with quality metrics, and provenance tracking. [Full documentation](../skills/sma-pipeline/SKILL.md) --- ### sma-prep **Description:** SMA-seq library prep and reference management. Create reference files, | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-prep/SKILL.md` | # SMA-seq Preparation Skill Complete workflow for preparing and running SMA-seq experiments with Oxford Nanopore sequencing. [Full documentation](../skills/sma-prep/SKILL.md) --- ### sma-reference **Description:** SMA-seq reference sequence management. Create, validate, index, import/export | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-reference/SKILL.md` | # SMA Reference Management Centralized management of SMA-seq reference sequences with automatic indexing and validation. [Full documentation](../skills/sma-reference/SKILL.md) --- ### sma-seq **Description:** Modular SMA-seq analysis components for database operations, metadata | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-seq/SKILL.md` | # SMA-seq - Modular Analysis Components Modular components for Single-Molecule-Accuracy sequencing analysis. These building blocks can be used independently or combined for custom workflows. [Full documentation](../skills/sma-seq/SKILL.md) --- ### sma-viz **Description:** Multi-reference SMA-seq visualization. Subsamples reads, aligns to one | Property | Value | |----------|-------| | SKILL.md | `../skills/sma-viz/SKILL.md` | # SMA-seq Multi-Reference Visualization Compare SMA-seq reads against multiple reference sequences. Each reference gets its own IGV HTML report, and a summary dashboard compares alignment metrics across all references. [Full documentation](../skills/sma-viz/SKILL.md) --- ### sma-config-builder **Description:** Interactive web UI for building and editing SMA-seq configuration files | Property | Value | |----------|-------| | SKILL.md | `../skills/sma_config_builder/SKILL.md` | # SMA-seq Configuration Builder Interactive web UI for visually building and editing SMA-seq configuration files. [Full documentation](../skills/sma_config_builder/SKILL.md) --- ### smaseq-qc-dev **Description:** Run tests, lint, and validate the smaseq-qc package after code changes. Use when editing any file in smaseq-qc/, before pushing changes, or when reproducing a CI failure locally. | Property | Value | |----------|-------| | SKILL.md | `../skills/smaseq-qc-dev/SKILL.md` | # smaseq-qc Development Workflow Run this after making changes to the `smaseq-qc/` package. [Full documentation](../skills/smaseq-qc-dev/SKILL.md) --- ### tapestation-sampling **Description:** Predict CRISPR/Cas9 enrichment yield from TapeStation DNA quality metrics. | Property | Value | |----------|-------| | SKILL.md | `../skills/tapestation-sampling/SKILL.md` | # TapeStation Sampling Probability Analysis Predict how many DNA molecules in a HMW input will span a CRISPR/Cas9 target locus, based on TapeStation quality metrics. [Full documentation](../skills/tapestation-sampling/SKILL.md) --- ### test-lib **Description:** Run and manage the test suite for SMA-seq lib/ modules. Supports targeting | Property | Value | |----------|-------| | SKILL.md | `../skills/test-lib/SKILL.md` | # Test Lib Modules Run pytest against the SMA-seq `lib/` module test suite. [Full documentation](../skills/test-lib/SKILL.md) --- ### viz-automation **Description:** | Property | Value | |----------|-------| | SKILL.md | `../skills/viz-automation/SKILL.md` | # viz-automation Skill Automated visualization generation for lab repositories. Detects repository type and generates appropriate visualizations: methodology diagrams, project overviews, and benchmark plots. [Full documentation](../skills/viz-automation/SKILL.md) --- ### workspace-porter **Description:** Export and restore Claude Code workspace configuration across machines. Use when migrating to a new computer or backing up configuration. | Property | Value | |----------|-------| | SKILL.md | `../skills/workspace-porter/SKILL.md` | # Workspace Porter Export and restore the entire Claude Code workspace configuration as a portable bundle. [Full documentation](../skills/workspace-porter/SKILL.md) ---