Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
Keywords:Bacterial genome assembly, Oxford Nanopore, Long-read sequencing, Hybrid assembly
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).
How to Cite
Copyright (c) 2022 Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
This work is licensed under a Creative Commons Attribution 4.0 International License.
Bill and Melinda Gates Foundation
Grant numbers OPP1175797