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Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.
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Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.
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gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants. For clinical pathogenicity use clinvar-database; for GWAS use gwas-database.
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Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.
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CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
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Chunked N-D arrays with compression and cloud storage. NumPy-style indexing. Backends: local, S3, GCS, ZIP, memory. Dask/Xarray integration for parallel and labeled computation. For lineage use lamindb; for labeled arrays use xarray.
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Implement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying. Use when building RAG systems, semantic search engines, or intelligent knowledge bases.
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Implement persistent memory patterns for AI agents using AgentDB. Includes session memory, long-term storage, pattern learning, and context management. Use when building stateful agents, chat systems, or intelligent assistants.
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Compute technical indicators like RSI, MACD, Bollinger Bands, SMA, EMA for a stock. Use when user asks about technical analysis, indicators, RSI, MACD, moving averages, overbought/oversold, or chart analysis.
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Background context for invoice-system input tax credit rules (仕入税額控除) in the shinkoku tax filing plugin. Contains eligibility requirements, the 6 permanent exceptions (帳簿のみ保存の恒久特例), transitional measures for purchases from tax-exempt businesses, and storage requirements. This skill is not user-invocable — Claude loads it automatically when responding to input tax credit questions under the invoice system.
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Provides structured AWS cost optimization guidance using five pillars (right-sizing, elasticity, pricing models, storage optimization, monitoring) and twelve actionable best practices with executable AWS CLI examples. Use when optimizing AWS costs, reviewing AWS spending, finding unused AWS resources, implementing FinOps practices, reducing EC2/EBS/S3 bills, configuring AWS Budgets, or performing AWS Well-Architected cost reviews.
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Provides AWS CloudFormation patterns for Amazon Bedrock resources including agents, knowledge bases, data sources, guardrails, prompts, flows, and inference profiles. Use when creating Bedrock agents with action groups, implementing RAG with knowledge bases, configuring vector stores, setting up content moderation guardrails, managing prompts, orchestrating workflows with flows, and configuring inference profiles for model optimization.
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Provides patterns for unit testing mappers, converters, and bean mappings. Validates entity-to-DTO and model transformation logic in isolation. Generates executable mapping tests with MapStruct and custom converter test coverage. Use when writing mapping tests, converter tests, entity mapping tests, or ensuring correct data transformation between DTOs and domain objects.
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Enables interaction with Google NotebookLM for advanced RAG (Retrieval-Augmented Generation) capabilities via the notebooklm-mcp-cli tool. Use when querying project documentation stored in NotebookLM, managing research notebooks and sources, retrieving AI-synthesized information, generating audio podcasts or reports from notebooks, or performing contextual queries against curated knowledge bases. Triggers on "notebooklm", "nlm", "notebook query", "research notebook", "query documentation in notebooklm".
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Provides unit test, integration test, and mock AI patterns for LangChain4j applications. Creates mock LLM responses, tests retrieval chains, validates RAG workflows, and implements Testcontainers-based integration tests for Java AI services. Use when unit testing AI services, integration testing LangChain4j components, mocking AI models, or testing LLM-based Java applications.
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Creates new Architecture Decision Record (ADR) documents for significant architectural changes using a consistent template and repository-aware naming and storage guidance. Use when a user or agent decides on an architectural change, needs to document technical rationale, or wants to add a new ADR to the project history.
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Provides integration patterns for LangChain4j with Spring Boot. Configures AI model beans, sets up chat memory with Spring context, integrates RAG pipelines with Spring Data, and handles auto-configuration, dependency injection, and Spring ecosystem integration. Use when embedding LangChain4j into Spring Boot applications, building Java LLM applications with @Bean configuration, or setting up Spring AI patterns.
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Provides chunking strategies for RAG systems. Generates chunk size recommendations (256-1024 tokens), overlap percentages (10-20%), and semantic boundary detection methods. Validates semantic coherence and evaluates retrieval precision/recall metrics. Use when building retrieval-augmented generation systems, vector databases, or processing large documents.
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Provides dependency injection patterns for Spring Boot projects, including constructor-first design, optional collaborator handling, bean selection, and wiring validation. Use when creating services and configurations, replacing field injection, or troubleshooting ambiguous or fragile Spring wiring.
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How to find and fix performance problems in Shift's desktop app. Use when something is slow, choppy, janky, or laggy (scrubbing, dragging, editing, undo, opening fonts), when profiling or measuring, when adding or reviewing perf tests, and before claiming a change made something faster.
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When the user wants to get press coverage, appear on podcasts, or build relationships with journalists and content creators. Also use when the user mentions "podcast guesting", "press outreach", "PR", "media exposure", "get on podcasts", or "journalist outreach".
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Convert construction data to/from Parquet format. Optimize storage, enable fast queries, and integrate with data lakehouses.
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Classify construction data by type (structured, unstructured, semi-structured). Analyze data sources and recommend appropriate storage/processing methods
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Track material deliveries, manage inventory, and coordinate logistics. Monitor delivery schedules and site storage.
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