Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.
PLoS Comput Biol
; 19(3): e1010905, 2023 03.
Article
in En
| MEDLINE
| ID: mdl-36862631
ABSTRACT
A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism's genome-each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, followed by other short-read polishing tools and manual curation. We also discuss potential pitfalls one might encounter when assembling challenging genomes, and we provide an online tutorial with sample data (github.com/rrwick/perfect-bacterial-genome-tutorial).
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Oryzias
/
Nanopores
Limits:
Animals
Language:
En
Journal:
PLoS Comput Biol
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
Year:
2023
Document type:
Article
Affiliation country:
Australia