「fast」の検索結果

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Than 2008) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.

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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo, Figshare, Dryad, and OSF.

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Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.

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Evaluates cardiovascular risk factors in persons receiving hormone therapy by obtaining fasting lipid profiles and diabetes screening. Triggered when a patient is on gender-affirming hormone therapy and due for routine cardiovascular risk assessment.

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Guide pre-endoscopy management decisions for patients on GLP-1 receptor agonists (semaglutide, tirzepatide, liraglutide etc.), deciding whether to proceed, delay, or modify the approach based on GI symptoms, fasting status, and indication. Trigger when a clinician asks about GLP-1 RA and endoscopy, semaglutide before colonoscopy, Ozempic before procedure, or whether to hold a GLP-1 agonist before endoscopy.

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A workflow skill that lets Codex keep coding for 60 hours on medium and large projects: Claude Code CLI plans through an interactive requirements questionnaire, PRD, specs, and roadmap; Codex implements verified vertical slices, with resumable Long-Run Execution for lengthy work; Trellis maintains project memory. Use when the user mentions 大项目工作流, Codex 连续开发 60 小时, Codex 长任务, long-running or resumable Codex implementation, large/medium project, new SaaS, multi-module system, requirements questionnaire, Claude Code CLI planning, Codex implementation handoff, Trellis bootstrap, non-system-drive project, or vertical slice. Skip for: single-file edits, casual Q&A, copy polish, throwaway prototypes, or tasks the user explicitly wants done fast without process.

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Vitest fast unit testing framework powered by Vite with Jest-compatible API. Use when writing tests, mocking, configuring coverage, or working with test filtering and fixtures.

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Use for Fermi estimation, or when a rough number is needed fast: "roughly how many...", "ballpark the cost", "estimate capacity or market size", "is this even feasible?". Decomposes, uses ranges and sanity-checks. Skip when exact data is available or a precise calculation is wanted.

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Unsloth: 2-5x faster LoRA/QLoRA fine-tuning, less VRAM.

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Fast Apple Mail search via SQLite on macOS.

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Fastest private buses (5-6h core, 6-8h w/ borders).

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Auto-transcribe voice messages using faster-whisper (local, no API key needed).

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Expert-level radio astronomy covering radio telescopes, interferometry, VLBI, pulsars, spectral line observations, fast radio bursts, and aperture synthesis imaging.

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Diagnoses and fixes UI performance across loading speed, rendering, animations, images, and bundle size. Use when the user mentions slow, laggy, janky, performance, bundle size, load time, or wants a faster, smoother experience.

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Design relational database schemas (and choose when to go NoSQL) that stay maintainable and fast. Use this skill whenever the user mentions tables, DDL, entities and relationships, normalization (1NF/2NF/3NF), primary and foreign keys, UUID vs bigint IDs, indexes (B-tree, composite, covering, partial), EXPLAIN, constraints (CHECK, UNIQUE, exclusion), transactions and isolation levels, migrations (Alembic, Prisma, Flyway, expand-contract, backfilling), or SQL vs NoSQL (MongoDB, DynamoDB, Cassandra, graph databases). Also trigger for "design the database", "model this domain", "which database should I use", or writing ORM models and migration files for PostgreSQL, MySQL, SQLite, or SQL Server.

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Plan, write, and maintain automated tests in any language, with worked examples in Python and JavaScript/TypeScript. Use this skill whenever the user wants to write or plan tests, apply TDD (red-green-refactor), structure unit tests with arrange-act-assert and given-when-then naming, choose between fakes, stubs, and mocks, set up dependency injection for testability, build integration tests with testcontainers, database seeding, or transaction rollback, write Playwright or Cypress end-to-end tests, use property-based testing with Hypothesis or fast-check, create pytest fixtures or factory_boy factories, review coverage or mutation testing, or triage flaky tests in CI. Also trigger for "test pyramid", "test trophy", "test isolation", "mocking", "snapshot tests", "golden files", "parametrized tests", "make the tests pass".

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。