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Identifies and fixes common Rust anti-patterns. Use during code review, when seeing excessive clones/unwraps/index loops, or when code fights the borrow checker instead of working with it.

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UI brief 生成 SKILL — 從 docs/keep.summary.md、正式規格書、task shard、cross-reference-index 與參考圖整理成可執行的 UI brief 或 task-ready brief。USE FOR: 新 UI 畫面開工前、既有畫面補 task shard 欄位、需要收斂 family / proof / normalized recipe / content_contract / smoke_route。DO NOT USE FOR: 直接修改 ui-spec JSON、直接做視覺 QA。

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Azure AI Search SDK for Python. Use for vector search, hybrid search, semantic ranking, indexing, and skillsets.

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Azure AI Projects SDK for Java. High-level SDK for Azure AI Foundry project management including connections, datasets, indexes, and evaluations.

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Azure AI Projects SDK for .NET. High-level client for Azure AI Foundry projects including agents, connections, datasets, deployments, evaluations, and indexes.

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Expert patterns for Algolia search implementation, indexing strategies, React InstantSearch, and relevance tuning Use when: adding search to, algolia, instantsearch, search api, search functionality.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.

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Programmatic SEO planning and analysis for pages generated at scale from data sources. Covers template engines, URL patterns, internal linking automation, thin content safeguards, and index bloat prevention. Use when user says "programmatic SEO", "pages at scale", "dynamic pages", "template pages", "generated pages", or "data-driven SEO".

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Comprehensive SEO analysis for any website or business type. Full site audits, single-page analysis, technical SEO (crawlability, indexability, Core Web Vitals with INP), schema markup, content quality (E-E-A-T), image optimization, sitemap analysis, and GEO for AI Overviews/ChatGPT/Perplexity. Industry detection for SaaS, e-commerce, local, publishers, agencies. Triggers on: SEO, audit, schema, Core Web Vitals, sitemap, E-E-A-T, AI Overviews, GEO, technical SEO, content quality, page speed.

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Locate CEconItemView::operator= in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the WeaponPaints gamedata entry "CEconItemView::operator=" (symbol CEconItemView_operator=). Copy-assignment operator. Shortlist via call sites in weapon-give/refresh paths that copy an existing CEconItemView into another (this-pointer copy of definition index, seed, wear, attribute list and item ID fields — a field-by-field copy, not a memcpy). Trigger: CEconItemView_operator=, CEconItemView::operator=

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Locate CEconItemView::CEconItemView in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the WeaponPaints gamedata entry "CEconItemView::CEconItemView" (symbol CEconItemView_CEconItemView). This is the CONSTRUCTOR of CEconItemView. Shortlist via allocation sites: callers of operator-new whose result is immediately stored with the CEconItemView vtable (RTTI), followed by zeroing and initialization of definition-index/quantity/attribute-list fields. Distinguish from subobject constructors of derived classes by the vtable identity. Trigger: CEconItemView_CEconItemView, CEconItemView::CEconItemView

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Locate CCSPlayerInventory::GetItemInLoadout in CS2 server.dll / libserver.so via IDA Pro MCP and emit a fresh, minimal-unique signature or offset for the WeaponPaints gamedata entry "CCSPlayerInventory::GetItemInLoadout" (symbol CCSPlayerInventory_GetItemInLoadout). Non-virtual inventory method resolving a player's loadout item. Shortlist via callers inside CCSPlayerInventory code that walk the loadout item cache (m_pSOCache / CGCClientSharedObjectCache), and via the CSO/econ loadout message paths. The function takes an item definition index + loadout slot and returns the matching CEconItemView — the body iterates a small item list comparing definition indices and loadout slots. Trigger: CCSPlayerInventory_GetItemInLoadout, CCSPlayerInventory::GetItemInLoadout

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