Preprint / Version 1

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

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DOI:

https://doi.org/10.1590/SciELOPreprints.5053

Keywords:

Bacterial genome assembly, Oxford Nanopore, Long-read sequencing, Hybrid assembly

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 of any scale. 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 with 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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Posted

11/11/2022

How to Cite

Wick, R. R., Judd, L. M., & Holt, K. E. (2022). Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. In SciELO Preprints. https://doi.org/10.1590/SciELOPreprints.5053

Section

Biological Sciences

Funding data

Plaudit