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 as...
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doaj-740f7969f10d4909b1310e844a757def2021-09-19T11:57:45ZengBMCGenome Biology1474-760X2021-09-0122111710.1186/s13059-021-02483-zTrycycler: consensus long-read assemblies for bacterial genomesRyan R. Wick0Louise M. Judd1Louise T. Cerdeira2Jane Hawkey3Guillaume Méric4Ben Vezina5Kelly L. Wyres6Kathryn E. Holt7Department of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityDepartment of Infectious Diseases, Central Clinical School, Monash UniversityAbstract 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.https://doi.org/10.1186/s13059-021-02483-zGenome assemblyBacterial genomicsWhole-genome sequencingLong-read sequencingOxford Nanopore sequencing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ryan R. Wick Louise M. Judd Louise T. Cerdeira Jane Hawkey Guillaume Méric Ben Vezina Kelly L. Wyres Kathryn E. Holt |
spellingShingle |
Ryan R. Wick Louise M. Judd Louise T. Cerdeira Jane Hawkey Guillaume Méric Ben Vezina Kelly L. Wyres Kathryn E. Holt Trycycler: consensus long-read assemblies for bacterial genomes Genome Biology Genome assembly Bacterial genomics Whole-genome sequencing Long-read sequencing Oxford Nanopore sequencing |
author_facet |
Ryan R. Wick Louise M. Judd Louise T. Cerdeira Jane Hawkey Guillaume Méric Ben Vezina Kelly L. Wyres Kathryn E. Holt |
author_sort |
Ryan R. Wick |
title |
Trycycler: consensus long-read assemblies for bacterial genomes |
title_short |
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_sort |
trycycler: consensus long-read assemblies for bacterial genomes |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2021-09-01 |
description |
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. |
topic |
Genome assembly Bacterial genomics Whole-genome sequencing Long-read sequencing Oxford Nanopore sequencing |
url |
https://doi.org/10.1186/s13059-021-02483-z |
work_keys_str_mv |
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