Read Length and Repeat Resolution Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies 英文参考文献.docVIP
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Read Length and Repeat Resolution Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies 英文参考文献
ReadLengthandRepeatResolution:Exploring
ProkaryoteGenomesUsingNext-GenerationSequencing
Technologies
MattJ.Cahill1,ClaudioU.Ko¨ser1,NicholasE.Ross2,JohnA.C.Archer3*
1DepartmentofGenetics,UniversityofCambridge,Cambridge,UnitedKingdom,2DepartmentofChemicalEngineeringandBiotechnology,UniversityofCambridge,
Cambridge, United Kingdom, 3Division of Chemical and Biological Engineering, Computational Bioscience Research Center, King Abdullah University of Science and
Technology,Thuwal,SaudiArabia
Abstract
Background:Thereareagrowingnumberofnext-generationsequencingtechnologies.Atpresent,themostcost-effective
optionsalsoproducetheshortestreads.However,evenforprokaryotes,thereisuncertaintyconcerningtheutilityofthese
technologiesforthedenovoassemblyofcompletegenomes.Thisreflectsanexpectationthatshortreadswillbeunableto
resolvesmall,butpresumablyabundant,repeats.
Methodology/PrincipalFindings:Usingasimplemodelofrepeatassembly,wedevelopandtestatechniquethat,forany
readlength,canestimatetheoccurrenceofunresolvablerepeatsinagenome,andthuspredictthenumberofgapsthat
wouldneedtobeclosedtoproduceacompletesequence.Weapplythistechniqueto818prokaryotegenomesequences.
This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only
150ntcanreconstructapproximately50%oftheanalysedgenomeswithfewerthan96repeat-inducedgaps.Nonetheless,
thereisconsiderablevariationamongstprokaryotes.Somegenomescanbeassembledtonearcontiguityusingveryshort
readswhileothersrequiremuchlongerreads.
Conclusions:Giventhediversityofprokaryotegenomes,asequencingstrategyshouldbetailoredtotheorganismunder
study.Ourresultswillprovideresearcherswithapracticalresourcetoguidetheselectionoftheappropriatereadlength.
Citation:CahillMJ,Ko¨serCU,RossNE,ArcherJAC(2010)ReadLengthandRepeatResolution:ExploringProkaryoteGenomesUsingNext-GenerationSequencing
Technologies.PLoSONE5(7):e11518.doi:10.1371/journal.pone.0011518
Editor:WenjunLi,DukeUniversityMedicalCenter,UnitedStatesof
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