Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

Detalhes bibliográficos
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
Resumo: 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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spelling Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencingBacterial genome assemblyOxford NanoporeLong-read sequencingHybrid assemblyA 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).SciELO PreprintsSciELO PreprintsSciELO Preprints2022-11-11info:eu-repo/semantics/preprintinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://preprints.scielo.org/index.php/scielo/preprint/view/505310.1590/SciELOPreprints.5053enghttps://preprints.scielo.org/index.php/scielo/article/view/5053/9840Copyright (c) 2022 Ryan R. Wick, Louise M. Judd, Kathryn E. Holthttps://creativecommons.org/licenses/by/4.0info:eu-repo/semantics/openAccessWick, Ryan R.Judd, Louise M.Holt, Kathryn E.reponame:SciELO Preprintsinstname:SciELOinstacron:SCI2022-11-11T03:05:35Zoai:ops.preprints.scielo.org:preprint/5053Servidor de preprintshttps://preprints.scielo.org/index.php/scieloONGhttps://preprints.scielo.org/index.php/scielo/oaiscielo.submission@scielo.orgopendoar:2022-11-11T03:05:35SciELO Preprints - SciELOfalse
dc.title.none.fl_str_mv Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
title Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
spellingShingle Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
Wick, Ryan R.
Bacterial genome assembly
Oxford Nanopore
Long-read sequencing
Hybrid assembly
title_short Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
title_full Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
title_fullStr Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
title_full_unstemmed Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
title_sort Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
author Wick, Ryan R.
author_facet Wick, Ryan R.
Judd, Louise M.
Holt, Kathryn E.
author_role author
author2 Judd, Louise M.
Holt, Kathryn E.
author2_role author
author
dc.contributor.author.fl_str_mv Wick, Ryan R.
Judd, Louise M.
Holt, Kathryn E.
dc.subject.por.fl_str_mv Bacterial genome assembly
Oxford Nanopore
Long-read sequencing
Hybrid assembly
topic Bacterial genome assembly
Oxford Nanopore
Long-read sequencing
Hybrid assembly
description 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).
publishDate 2022
dc.date.none.fl_str_mv 2022-11-11
dc.type.driver.fl_str_mv info:eu-repo/semantics/preprint
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format preprint
status_str publishedVersion
dc.identifier.uri.fl_str_mv https://preprints.scielo.org/index.php/scielo/preprint/view/5053
10.1590/SciELOPreprints.5053
url https://preprints.scielo.org/index.php/scielo/preprint/view/5053
identifier_str_mv 10.1590/SciELOPreprints.5053
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv https://preprints.scielo.org/index.php/scielo/article/view/5053/9840
dc.rights.driver.fl_str_mv Copyright (c) 2022 Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
https://creativecommons.org/licenses/by/4.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Copyright (c) 2022 Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
https://creativecommons.org/licenses/by/4.0
eu_rights_str_mv openAccess
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dc.publisher.none.fl_str_mv SciELO Preprints
SciELO Preprints
SciELO Preprints
publisher.none.fl_str_mv SciELO Preprints
SciELO Preprints
SciELO Preprints
dc.source.none.fl_str_mv reponame:SciELO Preprints
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instacron:SCI
instname_str SciELO
instacron_str SCI
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repository.mail.fl_str_mv scielo.submission@scielo.org
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