Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

Handle URI:
http://hdl.handle.net/10754/325284
Title:
Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies
Authors:
Cahill, Matt J.; Köser, Claudio U.; Ross, Nicholas E.; Archer, John A.C. ( 0000-0002-3302-3933 )
Abstract:
Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Cahill MJ, Köser CU, Ross NE, Archer JAC (2010) Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies. PLoS ONE 5: e11518. doi:10.1371/journal.pone.0011518.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
12-Jul-2010
DOI:
10.1371/journal.pone.0011518
PubMed ID:
20634954
PubMed Central ID:
PMC2902515
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorCahill, Matt J.en
dc.contributor.authorKöser, Claudio U.en
dc.contributor.authorRoss, Nicholas E.en
dc.contributor.authorArcher, John A.C.en
dc.date.accessioned2014-08-27T09:44:52Z-
dc.date.available2014-08-27T09:44:52Z-
dc.date.issued2010-07-12en
dc.identifier.citationCahill MJ, Köser CU, Ross NE, Archer JAC (2010) Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies. PLoS ONE 5: e11518. doi:10.1371/journal.pone.0011518.en
dc.identifier.issn19326203en
dc.identifier.pmid20634954en
dc.identifier.doi10.1371/journal.pone.0011518en
dc.identifier.urihttp://hdl.handle.net/10754/325284en
dc.description.abstractBackground: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.rightsCahill et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectaccuracyen
dc.subjectalgorithmen
dc.subjectbacterial genomeen
dc.subjectEscherichia coli K 12en
dc.subjectgenetic variabilityen
dc.subjectMycoplasma genitaliumen
dc.subjectnucleotide sequenceen
dc.subjectpredictionen
dc.subjectprokaryoteen
dc.subjectquantitative analysisen
dc.subjectsequence analysisen
dc.subjectspecies differenceen
dc.subjectStreptomyces coelicoloren
dc.subjectDNA sequenceen
dc.subjectgeneticsen
dc.subjectgenomeen
dc.subjectmetabolismen
dc.subjectmethodologyen
dc.subjectnucleotide repeaten
dc.subjectprokaryotic cellen
dc.subjectProkaryotaen
dc.subjectAlgorithmsen
dc.subjectGenomeen
dc.subjectProkaryotic Cellsen
dc.subjectRepetitive Sequences, Nucleic Aciden
dc.subjectSequence Analysis, DNAen
dc.titleRead length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologiesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC2902515en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Genetics, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.institutionDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorArcher, John A.C.en

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