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Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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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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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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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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THE full UI surface checklist (S1–S18) run on one assigned surface. Use for a named surface check, `/surface-check <surface>`, or a claimed `surface-certification` Work Loop item. NOT for fleet selection or claims (use surface-certification-loop).

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Use when modifying anything under features/files/, app/(core)/files/, app/(public)/share/, or any caller that uploads, downloads, lists, moves, renames, shares, or previews user files.

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Custom-entry fix for pickers with no way to add a choice (Select, Popover list, DropdownMenu). Use when building or touching any choice control (tier, category, tag, status, owner), `pnpm check:picker-add` names a file, running Pattern Patrol P13, or the user says 'no way to add my own' or 'why can't I type a new one'.

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react-resizable-panels v4 rules for this SSR codebase. Use when importing react-resizable-panels (PanelGroup and PanelResizeHandle are v3 names), editing components/ui/resizable* or features/code/layout/, building a split-pane, sidebar, or drag-handle layout, or persisting or toggling panel sizes.

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Pattern Patrols system of recurring, certified sweeps. Use when you are a patrol run or an assignment names a P# id, you spot a registered-pattern violation off-mission (log a sighting), a mistake class keeps recurring, or you touch PATROL_REGISTRY or PATROL_SIGHTINGS. NOT for one-off bug fixes.

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Run the full on-track check on a conversation, project, or keyword the owner names: find the sessions, extract exactly what he typed, dispatch independent judges who go to the live product as him and report what was missed, plan the remedy, and return one page — what he will see, what is missing, the plan. Use when told to check whether work is on track, to audit a project that has drifted, on 'run the on-track check on X', or when a long campaign is about to freeze, hand off, or claim done.

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Runbook for creating or majorly growing an @ai-matrx TypeScript npm package. Use when invoked as /new-package <name or capability>, or for a new @ai-matrx/* package, extracting code into one, or a major growth wave. NOT for a routine fix inside an existing package (THE SAME-SESSION LAW).

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Workflow for classifying AI Matrx server log lines in features/server-logs/log-rules.ts. Use when examining raw server logs, new [ModuleName] bracket tokens appear unclassified, log categories are wrong, or adding module recognition to the log viewer.

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The recipe for production-grade AI Matrx platform agents built through the AI Dream MCP. Use when asked to create, build, configure, improve, rename, or re-instruct a platform agent, or when a deliverable or kind needs an agent to emit it. NOT for Claude Code subagents or .claude/agents files.

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Disclosing a surface's existing fixed AI jobs in the shell's top Agents menu. Use when a page, panel, overlay, or window already runs a mandate behind a button, assist, automatic action, or mode; when the agent-disclosure guard names a file; or during a surface check.

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Migrating custom icon buttons to TapButtons. Use when replacing a raw <button>, IconButton, or className-styled icon; migrating header, toolbar, or footer icons; lazy-splitting a button's highlight decoration; or on 'tap targets', 'efficiency update', 'lazy split', or making a small component production-ready.

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Find and identify the CDecoyProjectile_Create factory in CS2 server binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the decoy projectile spawn factory. It is a non-virtual, direct-call static factory found via the entity classname string "decoy_projectile" it references (excluding the RTTI class string "CDecoyProjectile"). Emits a unique IDA-style byte signature and a func YAML. Mirrors the find-CDecoyProjectile_Create.py preprocessor (xref_strings FULLMATCH:decoy_projectile). Trigger: CDecoyProjectile_Create, CDecoyProjectile::Create, decoy projectile Create

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Batch-dump vtables from IDA Pro MCP by searching mangled symbol patterns, then write a merged YAML file beside the binary. Use this skill when you need to find and export all vtables matching a name pattern (e.g., all GameSystem vtables) in one shot. Triggers: dump vtables, batch vtable dump, export vtables, dump all vtables matching pattern

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The original v1 taste-skill, preserved for projects depending on its exact behavior. The current default is `design-taste-frontend` (v2 experimental), which is a substantial rewrite. Use this v1 install name only if you need exact backward compatibility.

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Preview Convex spend — rank functions by bytes/documents-read × call-volume from insights, project each cost driver's growth curve, name the cheapest fix; confirm-cost for paid actions.

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PSR-4 autoloading standard knowledge base for PHP 8.5 projects. Provides quick reference for namespace-to-path mapping, composer.json configuration, directory structure, and common mistakes. Use for autoloading audits and project structure reviews.

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