Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
Autor(a) principal: | |
---|---|
Data de Publicação: | 2022 |
Outros Autores: | , |
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). |
id |
SCI-1_42c559cfc65ea367aa574e7d64ce96f6 |
---|---|
oai_identifier_str |
oai:ops.preprints.scielo.org:preprint/5053 |
network_acronym_str |
SCI-1 |
network_name_str |
SciELO Preprints |
repository_id_str |
|
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 info:eu-repo/semantics/publishedVersion |
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 |
dc.format.none.fl_str_mv |
application/pdf |
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 instname:SciELO instacron:SCI |
instname_str |
SciELO |
instacron_str |
SCI |
institution |
SCI |
reponame_str |
SciELO Preprints |
collection |
SciELO Preprints |
repository.name.fl_str_mv |
SciELO Preprints - SciELO |
repository.mail.fl_str_mv |
scielo.submission@scielo.org |
_version_ |
1797047830531014656 |