Browse Skills — Page 129

gemini-automation

ComposioHQ/awesome-claude-skills

"Automate Gemini tasks via Rube MCP (Composio). Always search tools first for current schemas."

gemini-cli

TerminalSkills/skills

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gemini-count-in-video

elizaOS/eliza

Analyze and count objects in videos using Google Gemini API (object counting, pedestrian detection, vehicle tracking, and surveillance video analysis).

gemini-deep-research

terrylica/cc-skills

Run Gemini Deep Research via browser automation. Persistent Chrome on CDP port 9222. Use when user asks to research a topic with.

gemini-image-generator

notque/vexjoy-agent

Generate images from text prompts via Google Gemini.

gemini-review

alinaqi/maggy

Google Gemini CLI code review with Gemini 2.5 Pro, 1M token context, CI/CD integration

gemini-search

wanshuiyin/Auto-claude-code-research-in-sleep

Search research papers via Gemini for broad literature discovery. Use when user says "gemini search", "gemini papers", "search with gemini", or wants AI-powered literature discovery beyond arXiv/Semantic Scholar indexes.

gemini-tts

sonichi/sutando

Render text to mp3 via Google Gemini Flash TTS. Free-tier eligible (1500 req/day). Use for video narration, demo voiceovers, audio notes. Parallels openai-tts; default for make-viral-video.

gemini-video-understanding

elizaOS/eliza

Analyze videos with Google Gemini API (summaries, Q&A, transcription with timestamps + visual context, scene/timeline detection, video clipping, FPS control, multi-video comparison, and YouTube URL analysis).

gemini-webhooks

hookdeck/webhook-skills

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gen-release-notes

existential-birds/beagle

generate release notes for changes since a given tag

gen-specs-as-issues

github/awesome-copilot

'This workflow guides you through a systematic approach to identify missing features, prioritize them, and create detailed specifications for implementation.'

gen-test-plan

existential-birds/beagle

Analyze repo, detect stack, trace changes to user-facing entry points, generate E2E YAML test plan

gender-api-automation

ComposioHQ/awesome-claude-skills

"Automate Gender API tasks via Rube MCP (Composio). Always search tools first for current schemas."

genderapi-io-automation

ComposioHQ/awesome-claude-skills

"Automate Genderapi IO tasks via Rube MCP (Composio). Always search tools first for current schemas."

genderize-automation

ComposioHQ/awesome-claude-skills

"Automate Genderize tasks via Rube MCP (Composio). Always search tools first for current schemas."

gene_comprehensive_lookup

InternScience/scp

Gene Comprehensive Lookup - Comprehensive gene lookup: NCBI gene data, Ensembl gene info, UniProt protein data, and KEGG pathway links. Use this skill for bioinformatics tasks involving get gene metadata by gene name get lookup symbol get general info by protein or gene name kegg find. Combines 4 tools from 4 SCP server(s).

gene_disease_association

InternScience/scp

Gene-Disease Association Analysis - Analyze gene-disease associations: NCBI gene metadata, OpenTargets disease associations, TCGA expression, and Monarch phenotypes. Use this skill for medical genetics tasks involving get gene metadata by gene name get associated targets by disease efoId get gene expression across cancers get joint associated diseases by HPO ID list. Combines 4 tools from 4 SCP server(s).

gene_expression_atlas

InternScience/scp

Gene Expression Atlas - Build gene expression atlas: TCGA cancer expression, NCBI gene info, Ensembl gene details, and literature search. Use this skill for transcriptomics tasks involving get gene expression across cancers get gene metadata by gene name get lookup symbol search literature. Combines 4 tools from 4 SCP server(s).

gene_family_evolution

InternScience/scp

Gene Family Evolution Analysis - Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. Use this skill for molecular evolution tasks involving get cafe genetree member symbol get homology symbol get genetree member symbol get taxonomy classification. Combines 4 tools from 1 SCP server(s).

gene_therapy_target

InternScience/scp

Gene Therapy Target Analysis - Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence. Use this skill for gene therapy tasks involving get gene metadata by gene name get vep hgvs Protein structure prediction ESMFold clinvar search. Combines 4 tools from 4 SCP server(s).

gene_to_drug_pipeline

InternScience/scp

Gene-to-Drug Discovery Pipeline - Full gene-to-drug pipeline: gene lookup, protein structure, binding pocket, virtual screening, and drug-likeness. Use this skill for translational medicine tasks involving get gene metadata by gene name pred protein structure esmfold run fpocket boltz binding affinity calculate mol drug chemistry. Combines 5 tools from 3 SCP server(s).

gene_variant_drug_nexus

InternScience/scp

Gene-Variant-Drug Nexus - Connect gene variants to drugs: variant effect, gene-disease link, drug associations, and clinical evidence. Use this skill for translational genomics tasks involving get vep hgvs get associated targets by disease efoId get associated drugs by target name clinvar search. Combines 4 tools from 3 SCP server(s).

gene-database

jaechang-hits/SciAgent-Skills

NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.

gene-info

aipoch/medical-research-skills

Retrieves comprehensive gene information including PubMed publication counts, NCBI summaries, and Ensembl transcript data. Supports batch processing and file input. Invoke when the user asks for gene details, publication statistics, or needs to analyze a list of genes.

gene-knowledge-integration

InternScience/scp

Given a gene symbol (e.g. TPMT), query 3 public databases (ClinGen CAR, PharmGKB, Monarch) to obtain gene registry info, FDA drug labels, clinical annotations, and gene-phenotype associations. Save all results into a JSON file.

gene-panel-design-agent

swaruplab/operon

AI-powered design of targeted gene panels for clinical and research applications including cancer diagnostics, pharmacogenomics, and rare disease testing.

gene-regulatory-networks-coexpression-networks

swaruplab/operon

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

gene-regulatory-networks-differential-networks

swaruplab/operon

Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

gene-regulatory-networks-grn-inference

swaruplab/operon

Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

gene-regulatory-networks-multiomics-grn

swaruplab/operon

Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

gene-regulatory-networks-perturbation-simulation

swaruplab/operon

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.

gene-regulatory-networks-scenic-regulons

swaruplab/operon

Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

gene-structure-mapper

aipoch/medical-research-skills

Use gene structure mapper for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

genebass-gene-burden-skill

openai/plugins

Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries

genehmigungspflicht-pruefung

Klotzkette/claude-fuer-deutsches-recht

Prüft, ob ein konkretes Rechtsgeschäft, eine Maßnahme oder eine Entscheidung des Betreuers der Genehmigung des Betreuungsgerichts bedarf (§§ 1848 ff. BGB) — etwa Grundstücksverkauf, Erbausschlagung, Heimvertragsabschluss, Wohnungsauflösung, freiheitsentziehende Maßnahmen. Lädt, wenn Schlagwörter wie „Genehmigung Betreuungsgericht\", „§ 1848 BGB\", „§ 1850 BGB\", „§ 1851 BGB\", „freiheitsentziehende Maßnahme\" oder „Heimvertrag\" auftreten.

general-counsel-advisor

alirezarezvani/claude-skills

General Counsel advisory for startups: contract review (MSA, SaaS, NDA, DPA, employment), IP strategy, term sheet decoding, and regulatory landscape mapping. Use when reviewing any contract or term sheet, deciding when to engage outside counsel, defining IP strategy, evaluating regulatory exposure (HIPAA, GDPR, FDA, fintech), or when user mentions general counsel, GC, legal review, contract risk, term sheet, IP assignment, or regulatory exposure. NOT a substitute for licensed counsel — surfaces questions to bring to qualified attorneys.

general-figure-guide

jaechang-hits/SciAgent-Skills

Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.

general-morphological-analysis

yogsoth-ai/de-anthropocentric-research-engine

Ritchey GMA: complete iterative morphological process

generalklauseln-pruefen

Klotzkette/claude-fuer-deutsches-recht

Prueft Generalklauseln wie Treu und Glauben (§ 242 BGB), gute Sitten (§ 138 BGB), billiges Ermessen, oeffentliches Interesse und Verhaeltnismaessigkeit. Gibt Indizien und Fallgruppen statt mechanischer Subsumtion. Warnt vor der Grenzen automatisierter Pruefung.

generate

alirezarezvani/claude-skills

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generate_commit_message

multigres/multigres-operator

generate semantic git commit messages

generate_podcast

obra/muse-skills

Compose and deliver audio content: a podcast episode, briefing, or narrated summary, with one or more voices, as an MP3. For voice messages, artifact audio, or reading supplied text aloud verbatim, use tts.

generate-agent-card

agentic-community/mcp-gateway-registry

Generate an A2A agent card JSON by analyzing agent source code in a folder or GitHub URL. Studies the code to detect agent name, skills, tools, auth, protocol, and generates a spec-compliant agent card.

generate-agents-md

openakita/openakita

"Generate or update AGENTS.md for the current project. Use when user asks to create project guidelines, initialize AGENTS.md, or standardize project conventions."

generate-analogy-set

lyndonkl/claude

Generates exactly 5 distinct intuitive framings for a given technical topic — one everyday analogy, one physical metaphor, one contrarian take, one historical angle, one counterfactual. Each framing is a short scaffold (not prose), paired with its archetype and a one-line framing statement. Use when the writer invokes the Intuition Builder agent, as the core generation step before mapping, stress-testing, novelty checking, and voice fitness. Trigger keywords: generate framings, analogies for, give me 5, intuitive angles, framing set.

generate-asset-actions

UKGovernmentBEIS/inspect_evals

Generate asset-actions.yaml from ASSETS.yaml by classifying assets into priority tiers. Use when the user asks to regenerate, update, or refresh the asset actions.

generate-blueprints

TheBushidoCollective/han

Deeply research all systems and create or update blueprints/ documentation for the entire codebase

generate-candidate-fields

yogsoth-ai/de-anthropocentric-research-engine

Propose 3-8 candidate research fields based on the full ActorProfile. When user wants to explore beyond their current stack, use other ActorProfile signals (intentionality, boundary) to determine exploration space. Free exploration within the boundary.

generate-canvas-app

microsoft/power-platform-skills

[DEPRECATED — use canvas-app instead] Generate a complete Power Apps canvas app.

generate-claudemd

notque/vexjoy-agent

Generate project-specific CLAUDE.md from repo analysis.

generate-codebook

Aperivue/medsci-skills

Generate a citable data dictionary / codebook from a tabular dataset (CSV/TSV/Excel/Parquet/Stata/SAS). Profiles every variable — role, type, units placeholder, level frequencies, range/quantiles, missingness — and emits codebook.md + codebook.json. Flags coded variables whose level meanings are unknown as [NEEDS DICTIONARY] rather than guessing them, feeding /define-variables and the dictionary-first workflow.

generate-custom-instructions-from-codebase

github/awesome-copilot

'Migration and code evolution instructions generator for GitHub Copilot. Analyzes differences between two project versions (branches, commits, or releases) to create precise instructions allowing Copilot to maintain consistency during technology migrations, major refactoring, or framework version upgrades.'

generate-cve-json

apache/magpie

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generate-epics

Fr-e-d/GAAI-framework

Translate product intent or a PRD into a small set of outcome-driven Epics (3–7 max). Activate when starting a new product, adding a significant feature domain, or breaking down a PRD into actionable user outcomes.

generate-greeting

harbor-framework/harbor

Generate a greeting message and write it to a file.

generate-idea

GRIND-Lab-Core/night_owl_research_agent

Generate and rank research ideas given a broad direction. Use when user input "brainstorm ideas", "generate research ideas", "what can we work on", or wants to explore a research area for publishable directions.

generate-image

K-Dense-AI/scientific-agent-skills

Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.

generate-image

github/awesome-copilot

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generate-mcp-app-ui

microsoft/power-platform-skills

Generate an MCP App widget (self-contained HTML) for an MCP tool. Describe the visual you want and paste your tool's test output. Use when user asks to create an MCP App, widget, or visual for a tool.

generate-openenv-env

huggingface/OpenEnv

Generate OpenEnv environments from a concrete use case (for example, "generate an env for the library textarena"). Use when asked to design or implement a new environment under envs/ by researching a target library/API, selecting matching OpenEnv examples, asking key implementation questions, and building models/client/server/openenv.yaml. Do not use for model training or evaluation tasks.

generate-project-plan

figma/mcp-server-guide

Generate a FigJam project plan board from a PRD plus codebase context. Interactive flow: research → propose sections → per-section deep research → per-section content + block-shape proposal → create FigJam → skeleton → fill → diagrams → wrap. Each content block (section, nested section, intro callout, table, multi-column text, sticky column, diagram section, metadata strip) has its own subskill reference file. Use when the user asks for 'project plan in FigJam', 'interactive project plan', '/generate-project-plan', or provides a PRD and wants per-section confirmation on content + rendering.

generate-protocol-diff

microsoft/WindowsProtocolTestSuites

Skill for generating diffs between different versions of protocol specifications.

generate-readme

microsoft/Agent365-Samples

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generate-report

dandye/ai-runbooks

"Save investigation findings to a markdown report file. Use after completing triage, enrichment, or investigation to create a permanent record. Generates timestamped files in ./reports/ directory."

generate-requirement-drafts

matlab/simulink-agentic-toolkit

Generates draft requirements from Simulink models. Use when drafting or updating requirement artifacts from a model. Prefers Requirements Toolbox (.slreqx) when available; falls back to structured YAML.

generate-research-brief

yogsoth-ai/de-anthropocentric-research-engine

Aggregate all accumulated context from the crystallization process into a structured ResearchBrief document. This is the final output artifact alongside the North Star — a comprehensive requirement context document for downstream research strategies.

generate-revision-ux

microsoft/amplifier-skill-revisioner

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generate-run-commands

microsoft/vscode

Generate or modify run commands for the current session. Use when the user wants to set up or update run commands that appear in the session's Run button.

generate-server-card

agentic-community/mcp-gateway-registry

Generate an MCP server card JSON (mcp-gateway-registry format) by analyzing server source code in a folder or GitHub URL. Studies code to detect server name, tools, transport, auth, and generates a registry-compatible config.

generate-showcase-from-video

flutter/website

Extracts YouTube transcripts and generates professional Flutter showcase blog posts in Markdown format. Use when you need to create a technical marketing case study from a video success story.

generate-sitemap

dandye/ai-runbooks

Generate hierarchical site structure and navigation maps. Creates visual representations of information architecture and content relationships.

generate-stories

Fr-e-d/GAAI-framework

Translate a single Epic into clear, actionable User Stories with explicit acceptance criteria. Activate when an Epic is defined and work needs to be prepared for Delivery execution.

generate-synthetic-data

hamelsmu/evals-skills

>

generate-taxonomy

dandye/ai-runbooks

Develop hierarchical classification systems. Creates parent-child categorical structures for content organization.

generate-testability-wrappers

microsoft/testfx

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generate-thesaurus

dandye/ai-runbooks

Generate controlled vocabulary thesaurus for content domains. Creates comprehensive thesauri with preferred terms, broader/narrower/related terms.

generate-validation-notebook

monte-carlo-data/mc-agent-toolkit

Generate SQL validation notebooks for dbt changes. Pass a GitHub PR URL or local dbt repo path.

generate2dmap

0x0funky/agent-sprite-forge

Generate and revise production-oriented 2D game maps with built-in image generation as the default visual asset source, choosing a visual model, runtime object model, collision model, art direction, and engine/export target. Use when Codex needs to create or integrate RPG maps, monster-taming maps, tactical arenas, battle backgrounds, side-scroller/parallax scenes, tilemaps, layered raster maps, clean HD hand-painted maps, pixel-inspired maps, prop packs, collision zones, walkable areas, or map previews.

generate2dsprite

0x0funky/agent-sprite-forge

Generate and postprocess general 2D game assets and animation sheets: pixel-art sprites, clean HD map props, creatures, characters, NPCs, spells, projectiles, impacts, props, summons, and transparent GIF exports. Use when Codex should infer the asset plan from a natural-language request, match a reference or map art style, call built-in `image_gen` for solid-magenta raw sheets, and use the local processor only for chroma-key cleanup, frame extraction, alignment, QC, and transparent exports.

generating-lattice

oaustegard/claude-skills

>-

generating-patches

oaustegard/claude-skills

Generates git patch files from codebase modifications for local application. Use when user mentions patch, diff, export changes, bring changes back, apply locally, or after editing uploaded codebases.

generating-threat-intelligence-reports

mukul975/Anthropic-Cybersecurity-Skills

>

generating-trading-signals

aAAaqwq/AGI-Super-Team

Multi-indicator signal generation system that analyzes price action using 7 technical indicators and produces composite BUY/SELL signals with confiden

generating-weaverse-project-json

Weaverse/shopify-hydrogen-skills

Use when generating Weaverse project export JSON for import into the Weaverse editor. Triggers on requests to create, build, or produce a Weaverse project JSON file from a site migration, design spec, page layout description, or existing export. Also use when converting section plans into importable project and pages data.

generative-engine-optimization

kostja94/marketing-skills

When the user wants to optimize for AI search visibility (ChatGPT, Claude, Perplexity, AI Overviews). Also use when the user mentions "GEO," "AEO," "generative engine optimization," "AI search visibility," "LLM optimization," "GitHub GEO," "Grokipedia," "optimize for ChatGPT," "AI Overviews," "Bing Copilot," "Yandex AI," "Perplexity optimization," "GEO strategy," or "AI search optimization." For third-party publishing strategy (which platforms to use), use parasite-seo. For GitHub repos, README, and Awesome lists, use github. For Medium.com only, use medium-posts. For Grokipedia edits, use grokipedia-recommendations. For traditional Google SERP strategy, use seo-strategy.

generator.equals

diegofrata/Generator.Equals

Guidance for using Generator.Equals — a C# source generator for auto-generating Equals, GetHashCode, operators, and Diff/Inequalities methods via attributes.

generic-phenotype-scoring

aipoch/medical-research-skills

Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular program. Use when a study centers on gene-set or feature-set definition, intersection with DEGs or candidate features, phenotype scoring, feature selection, diagnostic or stratification assessment, immune or cellular-resolution interpretation, network analysis, and optional orthogonal validation. Covers five study patterns (signature discovery, phenotype scoring, feature selection, immune/cellular interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

generic-space-extraction

yogsoth-ai/de-anthropocentric-research-engine

Extract shared abstract structure from two input spaces

genesis

danielmeppiel/genesis

>-

genesis-evals

danielmeppiel/genesis

>-

genetic_counseling_report

InternScience/scp

Genetic Counseling Variant Report - Generate variant report for genetic counseling: VEP, ClinVar, gene phenotype, and literature evidence. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get phenotype gene pubmed search. Combines 4 tools from 2 SCP server(s).

geniml

K-Dense-AI/scientific-agent-skills

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

genmedia

fal-ai-community/genmedia-cli

>

genome_annotation

InternScience/scp

Genome Annotation Pipeline - Annotate a genome: NCBI annotation report, Ensembl gene lookup, UCSC tracks, and KEGG pathway links. Use this skill for genomics tasks involving get genome annotation report get lookup symbol list tracks kegg link. Combines 4 tools from 4 SCP server(s).

genome-annotation-annotation-qc

swaruplab/operon

Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.

genome-annotation-annotation-transfer

swaruplab/operon

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

genome-annotation-eukaryotic-gene-prediction

swaruplab/operon

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

genome-annotation-functional-annotation

swaruplab/operon

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.

genome-annotation-ncrna-annotation

swaruplab/operon

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.