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JASPER: A fast genome polishing tool that improves accuracy of genome assemblies

Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies. Using the latest nanopore-based sequencers, we can generate enough data for the assembly of a human genome from a single flow cell. With the long-read data from these sequen...

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Detalles Bibliográficos
Autores principales: Guo, Alina, Salzberg, Steven L., Zimin, Aleksey V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10096238/
https://www.ncbi.nlm.nih.gov/pubmed/37000853
http://dx.doi.org/10.1371/journal.pcbi.1011032
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author Guo, Alina
Salzberg, Steven L.
Zimin, Aleksey V.
author_facet Guo, Alina
Salzberg, Steven L.
Zimin, Aleksey V.
author_sort Guo, Alina
collection PubMed
description Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies. Using the latest nanopore-based sequencers, we can generate enough data for the assembly of a human genome from a single flow cell. With the long-read data from these sequences, we can now routinely produce de novo genome assemblies in which half or more of a genome is contained in megabase-scale contigs. Assemblies produced from nanopore data alone, though, have relatively high error rates and can benefit from a process called polishing, in which more-accurate reads are used to correct errors in the consensus sequence. In this manuscript, we present a novel tool for genome polishing called JASPER (Jellyfish-based Assembly Sequence Polisher for Error Reduction). In contrast to many other polishing methods, JASPER gains efficiency by avoiding the alignment of reads to the assembly. Instead, JASPER uses a database of k-mer counts that it creates from the reads to detect and correct errors in the consensus. Our experiments demonstrate that JASPER is faster than alignment-based polishers, and both faster and more accurate than other k-mer based polishing methods. We also introduce the idea of using a polishing tool to create population-specific reference genomes, and illustrate this idea using sequence data from multiple individuals from Tokyo, Japan.
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spelling pubmed-100962382023-04-13 JASPER: A fast genome polishing tool that improves accuracy of genome assemblies Guo, Alina Salzberg, Steven L. Zimin, Aleksey V. PLoS Comput Biol Research Article Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies. Using the latest nanopore-based sequencers, we can generate enough data for the assembly of a human genome from a single flow cell. With the long-read data from these sequences, we can now routinely produce de novo genome assemblies in which half or more of a genome is contained in megabase-scale contigs. Assemblies produced from nanopore data alone, though, have relatively high error rates and can benefit from a process called polishing, in which more-accurate reads are used to correct errors in the consensus sequence. In this manuscript, we present a novel tool for genome polishing called JASPER (Jellyfish-based Assembly Sequence Polisher for Error Reduction). In contrast to many other polishing methods, JASPER gains efficiency by avoiding the alignment of reads to the assembly. Instead, JASPER uses a database of k-mer counts that it creates from the reads to detect and correct errors in the consensus. Our experiments demonstrate that JASPER is faster than alignment-based polishers, and both faster and more accurate than other k-mer based polishing methods. We also introduce the idea of using a polishing tool to create population-specific reference genomes, and illustrate this idea using sequence data from multiple individuals from Tokyo, Japan. Public Library of Science 2023-03-31 /pmc/articles/PMC10096238/ /pubmed/37000853 http://dx.doi.org/10.1371/journal.pcbi.1011032 Text en © 2023 Guo et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Guo, Alina
Salzberg, Steven L.
Zimin, Aleksey V.
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title_full JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title_fullStr JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title_full_unstemmed JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title_short JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
title_sort jasper: a fast genome polishing tool that improves accuracy of genome assemblies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10096238/
https://www.ncbi.nlm.nih.gov/pubmed/37000853
http://dx.doi.org/10.1371/journal.pcbi.1011032
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