bio-genome-assembly-assembly-polishing

Name: bio-genome-assembly-assembly-polishing
Rating: 5 (2 reviews)
Author: bg-szy

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 m

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Version Compatibility

Reference examples tested with: Racon 1.5+, medaka 2.0+, minimap2 2.26+, bwa 0.7.17+, samtools 1.19+, Polypolish 0.6+, pypolca 0.3+, Pilon 1.24+, Merqury 1.3+, meryl 1.4+.

Before using code patterns, verify installed versions match. If versions differ:

CLI: <tool> --version then <tool> --help to confirm flags

The medaka consensus model matters more than the medaka binary version: the model must match the basecaller + pore chemistry + caller mode + version (`

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