Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.

Ryan R Wick ORCID logo; Louise M Judd; Kathryn E Holt ORCID logo; (2023) Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLOS Computational Biology, 19 (3). e1010905-. ISSN 1553-734X DOI: 10.1371/journal.pcbi.1010905
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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).


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