Read length versus Depth of Coverage for Viral Quasispecies Reconstruction 英文参考文献.docVIP

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Read length versus Depth of Coverage for Viral Quasispecies Reconstruction 英文参考文献.doc

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Read length versus Depth of Coverage for Viral Quasispecies Reconstruction 英文参考文献

ReadlengthversusDepthofCoverageforViral QuasispeciesReconstruction OsvaldoZagordi1,MartinDa¨umer2,ChristianBeisel3,NikoBeerenwinkel3,4* 1InstituteofMedicalVirology,UniversityofZurich,Zurich,Switzerland,2InstituteofImmunologyandGenetics,Kaiserslautern,Germany,3DepartmentofBiosystems ScienceandEngineering,ETHZurich,Basel,Switzerland,4SIBSwissInstituteofBioinformatics,Basel,Switzerland Abstract Recentadvancementsofsequencingtechnologyhaveopenedupunprecedentedopportunitiesinmanyapplicationareas. Virussamplescannowbesequencedefficientlywithverydeepcoveragetoinferthegeneticdiversityoftheunderlying viruspopulations.Severalsequencingplatformswithdifferentunderlyingtechnologiesandperformancecharacteristicsare availableforviraldiversitystudies.Here,weinvestigatehowthedifferencesbetweentwocommonplatformsprovidedby 454/RocheandIlluminaaffectviraldiversityestimationandthereconstructionofviralhaplotypes.Usingamixtureoften HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencingcoverage,readlength,anderrorrate.Forfixedcosts,shortIlluminareadscanbegeneratedathighercoverage andallowfordetectingvariantsatlower frequencies.Theycanalsobesufficient toassess thediversityofthesample if sequencesaredissimilarenough,but,ingeneral,assemblyoffull-lengthhaplotypesisfeasibleonlywiththelonger454/ Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidanceforthedesignofviraldiversitystudies. Citation:ZagordiO,Da¨umer M,BeiselC,BeerenwinkelN(2012)ReadlengthversusDepthofCoverageforViralQuasispeciesReconstruction.PLoSONE7(10): e47046.doi:10.1371/journal.pone.0047046 Editor:ArtF.Y.Poon,BritishColumbiaCentreforExcellenceinHIV/AIDS,Canada ReceivedJune29,2012;AcceptedSeptember7,2012;PublishedOctober3,2012 Copyright: ? 2012 Zagordi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestri