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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Guides the creation of complete Spring Boot features following a structured, layer-by-layer workflow: entity, repository, service, controller, and tests. Applies Kotlin idioms, Bean Validation, and MockK test patterns throughout.

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Audit web pages for performance optimization following PageSpeed Insights guidelines. Use when analyzing page performance, optimizing web applications, reviewing performance metrics, implementing Core Web Vitals improvements, or when the user mentions page speed, performance optimization, Lighthouse scores, or Core Web Vitals.

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Guides agents through scorecards, outcomes, model profiles, and eval suites. Use when running /cc-scorecard or /cc:scorecard, measuring a deliverable, or checking workflow gates with suite-run.

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Guides agents through authoring BACKLOG.md and OpenSpec change folders. Use when running /cc-backlog or /cc:backlog, creating or appending backlog items, or preparing work for /cc-openspec. Delivery is skill openspec.

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Guides agents through Red-Green-Refactor with runner-captured evidence. Use when running /cc-tdd-cycle, writing tests before implementation, or Global TDD required is yes.

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Full-stack Convex development guidelines covering React, Vite, TypeScript, mutations, auth, design system, and documentation practices. Use when building features, writing Convex functions, or making code changes in this project.

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Guide for when to use and when not to use return validators in Convex functions. Use this skill whenever the user is writing Convex queries, mutations, or actions and needs guidance on return value validation. Also trigger when the user asks about Convex type safety, runtime validation, AI-generated Convex code, Convex AI rules, Convex security best practices, or when they're debugging return type issues in Convex functions. Trigger this skill when users mention "validators", "returns", "return type", or "exact types" in the context of Convex development. Also trigger when writing or reviewing Convex AI rules or prompts that instruct LLMs how to write Convex code.

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Writing style guide for technical content, social media, blog posts, READMEs, git commits, and developer documentation. Optimized to avoid AI detection patterns. Use when writing any content beyond code.

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One-time setup that gathers design context for your project and saves it to your AI config file. Run once to establish persistent design guidelines.

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Guide for building and refactoring a FastAPI + Prefect + PostgreSQL/pgvector analytics pipeline that extracts insights from chat data using LLM classification, embeddings, UMAP/HDBSCAN clustering, and narrative generation. Use this skill whenever working on this project's codebase — including adding features, refactoring, debugging, creating new endpoints, modifying pipeline stages, or reviewing architecture decisions. Also trigger when the user asks about project structure, stack decisions, async migration, or best practices for this specific system.

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You are a senior backend engineer operating production-grade services under strict architectural and reliability constraints. Use when routes, controllers, services, repositories, express middleware, or prisma database access.

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This skill enforces Sentry's blog writing standards across every post — whether you're helping an engineer write their first blog post or a marketer draft a product announcement.

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To access Anthropic's official brand identity and style resources, use this skill.

日本語の概要は準備中です。原文の説明を表示しています。

To access Anthropic's official brand identity and style resources, use this skill.

日本語の概要は準備中です。原文の説明を表示しています。

Guidelines for modern Avalonia UI layout using Zafiro.Avalonia, emphasizing shared styles, generic components, and avoiding XAML redundancy.

日本語の概要は準備中です。原文の説明を表示しています。

API documentation workflow for generating OpenAPI specs, creating developer guides, and maintaining comprehensive API documentation.

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Angular performance optimization and best practices guide. Use when writing, reviewing, or refactoring Angular code for optimal performance, bundle size, and rendering efficiency.

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Production-grade Android app development guide covering native (Kotlin/Java), cross-platform (Flutter, RN, KMM), and hybrid architectures.

日本語の概要は準備中です。原文の説明を表示しています。