De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

Abstract Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtaine...

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Autores principales:	Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/19ac5c0a91fc44f59fafe58742d4515e
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spelling	oai:doaj.org-article:19ac5c0a91fc44f59fafe58742d4515e2021-12-02T16:08:09ZDe novo yeast genome assemblies from MinION, PacBio and MiSeq platforms10.1038/s41598-017-03996-z2045-2322https://doaj.org/article/19ac5c0a91fc44f59fafe58742d4515e2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03996-zhttps://doaj.org/toc/2045-2322Abstract Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies using Oxford Nanopore MinION data have attracted much attention due to the portability and low cost of this novel sequencing instrument. In this paper, we re-sequenced a well characterized genome, the Saccharomyces cerevisiae S288C strain using three different platforms: MinION, PacBio and MiSeq. We present a comprehensive metric comparison of assemblies generated by various pipelines and discuss how the platform associated data characteristics affect the assembly quality. With a given read depth of 31X, the assemblies from both Pacific Biosciences and Oxford Nanopore MinION show excellent continuity and completeness for the 16 nuclear chromosomes, but not for the mitochondrial genome, whose reconstruction still represents a significant challenge.Francesca GiordanoLouise AigrainMichael A QuailPaul CouplandJames K BonfieldRobert M DaviesGerman TischlerDavid K JacksonThomas M KeaneJing LiJia-Xing YueGianni LitiRichard DurbinZemin NingNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Francesca Giordano Louise Aigrain Michael A Quail Paul Coupland James K Bonfield Robert M Davies German Tischler David K Jackson Thomas M Keane Jing Li Jia-Xing Yue Gianni Liti Richard Durbin Zemin Ning De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
description	Abstract Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies using Oxford Nanopore MinION data have attracted much attention due to the portability and low cost of this novel sequencing instrument. In this paper, we re-sequenced a well characterized genome, the Saccharomyces cerevisiae S288C strain using three different platforms: MinION, PacBio and MiSeq. We present a comprehensive metric comparison of assemblies generated by various pipelines and discuss how the platform associated data characteristics affect the assembly quality. With a given read depth of 31X, the assemblies from both Pacific Biosciences and Oxford Nanopore MinION show excellent continuity and completeness for the 16 nuclear chromosomes, but not for the mitochondrial genome, whose reconstruction still represents a significant challenge.
format	article
author	Francesca Giordano Louise Aigrain Michael A Quail Paul Coupland James K Bonfield Robert M Davies German Tischler David K Jackson Thomas M Keane Jing Li Jia-Xing Yue Gianni Liti Richard Durbin Zemin Ning
author_facet	Francesca Giordano Louise Aigrain Michael A Quail Paul Coupland James K Bonfield Robert M Davies German Tischler David K Jackson Thomas M Keane Jing Li Jia-Xing Yue Gianni Liti Richard Durbin Zemin Ning
author_sort	Francesca Giordano
title	De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
title_short	De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
title_full	De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
title_fullStr	De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
title_full_unstemmed	De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
title_sort	de novo yeast genome assemblies from minion, pacbio and miseq platforms
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/19ac5c0a91fc44f59fafe58742d4515e
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_version_	1718384579822223360

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

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