Results for “erasure”

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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Correct or withdraw specific saved Knowledge claims, explicit relationships, or pages at the user's request, preserving provenance and inspecting affected knowledge. Use for “that's wrong”, “retract that”, or a Knowledge chat reference; not automatic contradiction resolution or physical erasure.

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Use when you need to review, improve, or refactor Java code for generics quality — including avoiding raw types, applying the PECS (Producer Extends Consumer Super) principle for wildcards, using bounded type parameters, designing effective generic methods, leveraging the diamond operator, understanding type erasure implications, handling generic inheritance correctly, preventing heap pollution with @SafeVarargs, and integrating generics with modern Java features like Records, sealed types, and pattern matching. Part of the skills-for-java project

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