Trycycler: consensus long-read assemblies for bacterial genomes

While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies...

Descripción completa

Detalles Bibliográficos
Autores principales: Wick, Ryan R., Judd, Louise M., Cerdeira, Louise T., Hawkey, Jane, Méric, Guillaume, Vezina, Ben, Wyres, Kelly L., Holt, Kathryn E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442456/
https://www.ncbi.nlm.nih.gov/pubmed/34521459
http://dx.doi.org/10.1186/s13059-021-02483-z
_version_ 1783753011389005824
author Wick, Ryan R.
Judd, Louise M.
Cerdeira, Louise T.
Hawkey, Jane
Méric, Guillaume
Vezina, Ben
Wyres, Kelly L.
Holt, Kathryn E.
author_facet Wick, Ryan R.
Judd, Louise M.
Cerdeira, Louise T.
Hawkey, Jane
Méric, Guillaume
Vezina, Ben
Wyres, Kelly L.
Holt, Kathryn E.
author_sort Wick, Ryan R.
collection PubMed
description While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool. Post-assembly polishing further reduced errors and Trycycler+polishing assemblies were the most accurate genomes in our study. As Trycycler requires manual intervention, its output is not deterministic. However, we demonstrated that multiple users converge on similar assemblies that are consistently more accurate than those produced by automated assembly tools. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02483-z.
format Online
Article
Text
id pubmed-8442456
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-84424562021-09-15 Trycycler: consensus long-read assemblies for bacterial genomes Wick, Ryan R. Judd, Louise M. Cerdeira, Louise T. Hawkey, Jane Méric, Guillaume Vezina, Ben Wyres, Kelly L. Holt, Kathryn E. Genome Biol Software While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool. Post-assembly polishing further reduced errors and Trycycler+polishing assemblies were the most accurate genomes in our study. As Trycycler requires manual intervention, its output is not deterministic. However, we demonstrated that multiple users converge on similar assemblies that are consistently more accurate than those produced by automated assembly tools. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02483-z. BioMed Central 2021-09-14 /pmc/articles/PMC8442456/ /pubmed/34521459 http://dx.doi.org/10.1186/s13059-021-02483-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Wick, Ryan R.
Judd, Louise M.
Cerdeira, Louise T.
Hawkey, Jane
Méric, Guillaume
Vezina, Ben
Wyres, Kelly L.
Holt, Kathryn E.
Trycycler: consensus long-read assemblies for bacterial genomes
title Trycycler: consensus long-read assemblies for bacterial genomes
title_full Trycycler: consensus long-read assemblies for bacterial genomes
title_fullStr Trycycler: consensus long-read assemblies for bacterial genomes
title_full_unstemmed Trycycler: consensus long-read assemblies for bacterial genomes
title_short Trycycler: consensus long-read assemblies for bacterial genomes
title_sort trycycler: consensus long-read assemblies for bacterial genomes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442456/
https://www.ncbi.nlm.nih.gov/pubmed/34521459
http://dx.doi.org/10.1186/s13059-021-02483-z
work_keys_str_mv AT wickryanr trycyclerconsensuslongreadassembliesforbacterialgenomes
AT juddlouisem trycyclerconsensuslongreadassembliesforbacterialgenomes
AT cerdeiralouiset trycyclerconsensuslongreadassembliesforbacterialgenomes
AT hawkeyjane trycyclerconsensuslongreadassembliesforbacterialgenomes
AT mericguillaume trycyclerconsensuslongreadassembliesforbacterialgenomes
AT vezinaben trycyclerconsensuslongreadassembliesforbacterialgenomes
AT wyreskellyl trycyclerconsensuslongreadassembliesforbacterialgenomes
AT holtkathryne trycyclerconsensuslongreadassembliesforbacterialgenomes

Ejemplares similares