The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.

The introduction of third-generation DNA sequencing technologies in recent years has allowed scientists to generate dramatically longer sequence reads, which when used in whole-genome sequencing projects have yielded better repeat resolution and far more contiguous genome assemblies. While the promi...

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Autores principales:	Aleksey V Zimin, Steven L Salzberg
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2020
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8418bdb46e6b497ca5a7f445397cee26
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spelling	oai:doaj.org-article:8418bdb46e6b497ca5a7f445397cee262021-12-02T19:58:10ZThe genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.1553-734X1553-735810.1371/journal.pcbi.1007981https://doaj.org/article/8418bdb46e6b497ca5a7f445397cee262020-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1007981https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The introduction of third-generation DNA sequencing technologies in recent years has allowed scientists to generate dramatically longer sequence reads, which when used in whole-genome sequencing projects have yielded better repeat resolution and far more contiguous genome assemblies. While the promise of better contiguity has held true, the relatively high error rate of long reads, averaging 8-15%, has made it challenging to generate a highly accurate final sequence. Current long-read sequencing technologies display a tendency toward systematic errors, in particular in homopolymer regions, which present additional challenges. A cost-effective strategy to generate highly contiguous assemblies with a very low overall error rate is to combine long reads with low-cost short-read data, which currently have an error rate below 0.5%. This hybrid strategy can be pursued either by incorporating the short-read data into the early phase of assembly, during the read correction step, or by using short reads to "polish" the consensus built from long reads. In this report, we present the assembly polishing tool POLCA (POLishing by Calling Alternatives) and compare its performance with two other popular polishing programs, Pilon and Racon. We show that on simulated data POLCA is more accurate than Pilon, and comparable in accuracy to Racon. On real data, all three programs show similar performance, but POLCA is consistently much faster than either of the other polishing programs.Aleksey V ZiminSteven L SalzbergPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 16, Iss 6, p e1007981 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Aleksey V Zimin Steven L Salzberg The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
description	The introduction of third-generation DNA sequencing technologies in recent years has allowed scientists to generate dramatically longer sequence reads, which when used in whole-genome sequencing projects have yielded better repeat resolution and far more contiguous genome assemblies. While the promise of better contiguity has held true, the relatively high error rate of long reads, averaging 8-15%, has made it challenging to generate a highly accurate final sequence. Current long-read sequencing technologies display a tendency toward systematic errors, in particular in homopolymer regions, which present additional challenges. A cost-effective strategy to generate highly contiguous assemblies with a very low overall error rate is to combine long reads with low-cost short-read data, which currently have an error rate below 0.5%. This hybrid strategy can be pursued either by incorporating the short-read data into the early phase of assembly, during the read correction step, or by using short reads to "polish" the consensus built from long reads. In this report, we present the assembly polishing tool POLCA (POLishing by Calling Alternatives) and compare its performance with two other popular polishing programs, Pilon and Racon. We show that on simulated data POLCA is more accurate than Pilon, and comparable in accuracy to Racon. On real data, all three programs show similar performance, but POLCA is consistently much faster than either of the other polishing programs.
format	article
author	Aleksey V Zimin Steven L Salzberg
author_facet	Aleksey V Zimin Steven L Salzberg
author_sort	Aleksey V Zimin
title	The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
title_short	The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
title_full	The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
title_fullStr	The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
title_full_unstemmed	The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
title_sort	genome polishing tool polca makes fast and accurate corrections in genome assemblies.
publisher	Public Library of Science (PLoS)
publishDate	2020
url	https://doaj.org/article/8418bdb46e6b497ca5a7f445397cee26
work_keys_str_mv	AT alekseyvzimin thegenomepolishingtoolpolcamakesfastandaccuratecorrectionsingenomeassemblies AT stevenlsalzberg thegenomepolishingtoolpolcamakesfastandaccuratecorrectionsingenomeassemblies AT alekseyvzimin genomepolishingtoolpolcamakesfastandaccuratecorrectionsingenomeassemblies AT stevenlsalzberg genomepolishingtoolpolcamakesfastandaccuratecorrectionsingenomeassemblies
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The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.

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