Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

• Autor(a) principal: Wick, Ryan R.
• Data de Publicação: 2022
• Outros Autores: Judd, Louise M., Holt, Kathryn E.
• Tipo de documento: preprint
• Idioma: eng
• Título da fonte: SciELO Preprints
• Texto Completo: https://preprints.scielo.org/index.php/scielo/preprint/view/5053
• topic: 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).