domains / families / science / assembly-polishing

assembly-polishing

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Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.

When to use

• correcting homopolymer indels or residual SNPs in a long-read assembly
• deciding if a HiFi assembly needs polishing
• choosing an ONT vs hybrid vs short-read polishing chain
• applying read-type-matched polisher
• measuring gain with held-out k-mers

When not to use

• polishing HiFi assemblies by default
• scoring with the same reads used for polishing
• using BUSCO as a stop signal
• improving CCS reads upstream of assembly

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