How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.
Microb Genom
; 10(6)2024 Jun.
Article
en En
| MEDLINE
| ID: mdl-38833287
ABSTRACT
It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter). We then show that (1) all polishers other than Pypolca-careful, Polypolish-default and Polypolish-careful commonly introduce false-positive errors at low read depth; (2) most of the benefit of short-read polishing occurs by 25× depth; (3) Polypolish-careful almost never introduces false-positive errors at any depth; and (4) Pypolca-careful is the single most effective polisher. Overall, we recommend the following polishing strategies Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolca-careful when depth is low (5-25×), and Polypolish-default and Pypolca-careful when depth is sufficient (>25×).
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Base de datos:
MEDLINE
Asunto principal:
Genoma Bacteriano
Idioma:
En
Revista:
Microb Genom
Año:
2024
Tipo del documento:
Article
País de afiliación:
Australia