Results for “duplication”

Structured 6-step procedure for improving, renovating, or rebuilding existing pipelines, individual project folders, documentation structures, or software stacks. Addressable as "pipeline optimizer" (for whole topic pipelines, e.g. a software, research, or game-dev pipeline) or "project-folder optimizer" (for individual project folders within a pipeline, e.g. a single software tool or paper project). Triggers on tasks like "improve pipeline X", "optimize the stack", "rebuild Y", "renovation", "pipeline refactoring", "clean up project folder", "improve folder structure", "unify conventions", "documentation consolidation", "integrate into existing system", or any substantial intervention in established structures. Delivers building-stock analysis, purpose clarification, ideal sketch, gap plan, empirical pain-point identification, and retests with fresh subagents. Prevents parallel standards, duplication, and pipeline breaks.

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Analyze GTmetrix (and PageSpeed) reports for WordPress sites and produce a prioritized optimization plan, a custom WPCode-ready PHP optimization snippet, and a self-contained HTML summary report. Covers PDF report extraction with pypdf, live-page cross-referencing, WordPress-specific fix mapping (Elementor, WooCommerce, Breeze, reCAPTCHA, Google-tag duplication, WebP conversion), and staging-test discipline. Use when asked to review GTmetrix reports, optimize page speed or Core Web Vitals, create a custom performance optimization snippet, or produce an optimization report for a WordPress site.

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Audit server-side paid-media measurement including server-side tag management, platform conversion APIs, event taxonomy, browser/server deduplication, consent, hashing, data quality, observability, and privacy. Use for server-side tracking, sGTM, server-side tagging, CAPI, Events API, event_id, pixel debugging, first-party measurement, or conversion data loss.

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Performs architectural code reviews focusing on design patterns, duplication, circular dependencies, and refactoring impact. Is the design consistent with the codebase? Use when reviewing code changes for architectural concerns, code smells, or structural issues.

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Implements BLoC (v9.x) event-driven state management for Flutter with unidirectional data flow using the flutter_bloc package. Use when implementing Bloc/Cubit classes, mapping Events to States, consuming state with BlocBuilder/BlocListener/BlocConsumer, applying event transformers (restartable/droppable/sequential) for concurrency control, setting up BlocProvider/MultiBlocProvider DI, integrating Freezed for sealed union types and exhaustive pattern matching, or testing with blocTest. Ideal for enterprise apps requiring business logic separation, precise concurrency control (search debouncing, form deduplication), or event replay debugging.

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Use when: investigating a legacy, inherited, third-party-built, or otherwise newly-unfamiliar codebase before scoping a migration or major refactor. Formalizes a repeatable five-step investigation pass — entry-point census, business-rule classification, side-effect/idempotency cataloging, implicit-contract discovery, semantic-duplication detection — plus a canonical per-project Open Questions document. Requires checkable signals: ticket keywords or prior documentation gaps. Not a mandatory gate; reserved for entry-point-heavy work in code areas with no prior investigation record.

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Refactor Python code to improve quality while keeping functionality intact. Use when cleaning up complexity, removing duplication, or tightening structure.

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Build training datasets for LLM specialization from production data, frontier model distillation, and synthetic bootstrapping. Use when formatting production logs into SFT data, distilling from frontier APIs, or preparing data for fine-tuning. Covers JSONL formatting, data quality validation, deduplication, and train/eval splitting.

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Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware Poisson GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via the four-BAM-vector interface (bam_ip + bam_input control; bam_treated_ip + bam_treated_input treatment), ChIPseeker annotation, and the canonical Guitar metagene with stop-codon enrichment as the biological QC anchor. Use when running a complete MeRIP analysis from raw reads, when chaining the constituent epitranscriptomics skills (merip-preprocessing -> m6a-peak-calling -> m6a-differential -> modification-visualization), or when wrapping the pipeline in Snakemake / Nextflow.

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Two-phase memory hygiene. Phase 1: scan external Claude Code memory (~/.claude/projects/<slug>/memory/) for durable rules to migrate into the repo and entries already duplicated by repo atoms. Phase 2: audit in-repo memory/, CLAUDE.md, docs/architecture/, and docs/sections/ for dead links, duplication, drift, and bloat.

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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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Analyze a completed phase diff for high-confidence behavior-preserving simplifications and apply only explicitly approved proposals. Use after execution and before review to reduce duplication, dead code, needless complexity, or avoidable inefficiency.

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Refactor code to improve quality while maintaining functionality. Use when you need to improve code structure, eliminate duplication, optimize performance, or enhance maintainability without changing behavior.

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Simplify application code for clarity without changing behavior — refactor after tests pass, reduce nesting and duplication, match project conventions. Load when refactoring for readability, cleaning up after a feature ships, or when code review flags complexity. Also triggers on "simplify this code", "code simplification", "make this easier to read", "reduce complexity", "refactor for clarity". Not for compress/split/prune-skill (skill-library files). Pairs with technical-debt-audit.

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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Prepare high-quality datasets for LLM fine-tuning with filtering, deduplication, augmentation, and RLHF data formatting. Activate on: fine-tuning data, training data curation, RLHF dataset, data quality filtering, SFT dataset. NOT for: model training infrastructure (ai-engineer), prompt engineering without fine-tuning (prompt-engineer).

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Secures webhook receivers with signature verification, retry handling, deduplication, idempotency keys, and error responses. Provides verification code, dedupe storage strategy, runbook for incidents. Use when implementing "webhooks", "webhook security", "event receivers", or "third-party integrations".

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Converts documents into clean, chunked datasets suitable for embeddings and vector search. Produces chunked JSONL files with metadata, deduplication logic, and quality checks. Use when preparing "training data", "vector datasets", "document processing", or "embedding data".

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Week 2 of the exploit development curriculum. Covers fuzzing methodology: target selection, corpus generation, coverage-guided fuzzing with AFL++/libFuzzer, structured fuzzing, and triage/deduplication. Use when setting up fuzz campaigns, selecting harness strategies, or triaging fuzzer output.

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