Unlocking short read sequencing for metagenomics.

<h4>Background</h4>Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.<h4>Methodology/principal findings</h4&g...

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Autores principales:	Sébastien Rodrigue, Arne C Materna, Sonia C Timberlake, Matthew C Blackburn, Rex R Malmstrom, Eric J Alm, Sallie W Chisholm
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/531089d980f540f8b9efec40a55e69b3
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id	oai:doaj.org-article:531089d980f540f8b9efec40a55e69b3
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spelling	oai:doaj.org-article:531089d980f540f8b9efec40a55e69b32021-12-02T20:19:40ZUnlocking short read sequencing for metagenomics.1932-620310.1371/journal.pone.0011840https://doaj.org/article/531089d980f540f8b9efec40a55e69b32010-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20676378/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.<h4>Methodology/principal findings</h4>We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.<h4>Conclusions/significance</h4>This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.Sébastien RodrigueArne C MaternaSonia C TimberlakeMatthew C BlackburnRex R MalmstromEric J AlmSallie W ChisholmPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 7, p e11840 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sébastien Rodrigue Arne C Materna Sonia C Timberlake Matthew C Blackburn Rex R Malmstrom Eric J Alm Sallie W Chisholm Unlocking short read sequencing for metagenomics.
description	<h4>Background</h4>Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.<h4>Methodology/principal findings</h4>We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.<h4>Conclusions/significance</h4>This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.
format	article
author	Sébastien Rodrigue Arne C Materna Sonia C Timberlake Matthew C Blackburn Rex R Malmstrom Eric J Alm Sallie W Chisholm
author_facet	Sébastien Rodrigue Arne C Materna Sonia C Timberlake Matthew C Blackburn Rex R Malmstrom Eric J Alm Sallie W Chisholm
author_sort	Sébastien Rodrigue
title	Unlocking short read sequencing for metagenomics.
title_short	Unlocking short read sequencing for metagenomics.
title_full	Unlocking short read sequencing for metagenomics.
title_fullStr	Unlocking short read sequencing for metagenomics.
title_full_unstemmed	Unlocking short read sequencing for metagenomics.
title_sort	unlocking short read sequencing for metagenomics.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/531089d980f540f8b9efec40a55e69b3
work_keys_str_mv	AT sebastienrodrigue unlockingshortreadsequencingformetagenomics AT arnecmaterna unlockingshortreadsequencingformetagenomics AT soniactimberlake unlockingshortreadsequencingformetagenomics AT matthewcblackburn unlockingshortreadsequencingformetagenomics AT rexrmalmstrom unlockingshortreadsequencingformetagenomics AT ericjalm unlockingshortreadsequencingformetagenomics AT salliewchisholm unlockingshortreadsequencingformetagenomics
_version_	1718374165040332800

Unlocking short read sequencing for metagenomics.

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