Trycycler: consensus long-read assemblies for bacterial genomes

Ryan R. Wick; Louise M. Judd; Louise T. Cerdeira; Jane Hawkey; Guillaume Méric; Ben Vezina; Kelly L. Wyres; Kathryn E. Holt

doi:10.1186/s13059-021-02483-z

Trycycler: consensus long-read assemblies for bacterial genomes

Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt

Research output: Contribution to journal › Article › Research › peer-review

313 Citations (Scopus)

Abstract

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.

Original language	English
Article number	266
Number of pages	17
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02483-z
Publication status	Published - 14 Sept 2021

Keywords

Bacterial genomics
Genome assembly
Long-read sequencing
Oxford Nanopore sequencing
Whole-genome sequencing

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10.1186/s13059-021-02483-zLicence: CC BY

Cite this

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title = "Trycycler: consensus long-read assemblies for bacterial genomes",

abstract = "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.",

keywords = "Bacterial genomics, Genome assembly, Long-read sequencing, Oxford Nanopore sequencing, Whole-genome sequencing",

author = "Wick, \{Ryan R.\} and Judd, \{Louise M.\} and Cerdeira, \{Louise T.\} and Jane Hawkey and Guillaume M{\'e}ric and Ben Vezina and Wyres, \{Kelly L.\} and Holt, \{Kathryn E.\}",

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AU - Hawkey, Jane

AU - Méric, Guillaume

AU - Vezina, Ben

AU - Wyres, Kelly L.

AU - Holt, Kathryn E.

N1 - Funding Information: This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation [OPP1175797]. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. This work was also supported by an Australian Government Research Training Program Scholarship, and KEH is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Victoria. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/9/14

Y1 - 2021/9/14

N2 - 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.

AB - 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.

KW - Bacterial genomics

KW - Genome assembly

KW - Long-read sequencing

KW - Oxford Nanopore sequencing

KW - Whole-genome sequencing

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Trycycler: consensus long-read assemblies for bacterial genomes

Abstract

Keywords

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