Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data 英文参考文献.docVIP

EvaluatingtheFidelityofDeNovoShortRead MetagenomicAssemblyUsingSimulatedData MiguelPignatelli1,2,3*,Andre′sMoya1,2 1UnitatMixtad’Investigacio′ enGeno`micaiSalut,CentreSuperiord’Investigacio′ enSalutPu′blica/UVEG-InstitutCavanilles,Valencia,Spain,2CIBERenEpidemiolog?′ay SaludPu′blica(CIBERESP),Barcelona,Spain,3EuropeanBioinformaticsInstitute,WellcomeTrustGenomeCampus,Hinxton,UnitedKingdom Abstract Afrequentstepinmetagenomicdataanalysiscomprisestheassemblyofthesequencedreads.Manyassemblytoolshave been published in the last years targeting data coming from next-generation sequencing (NGS) technologies but these assemblershavenotbeendesignedforortestedinmulti-genomescenariosthatcharacterizemetagenomicstudies.Here weprovideacriticalassessmentofcurrentdenovoshortreadsassemblytoolsinmulti-genomescenariosusingcomplex simulated metagenomic data. With this approach we tested the fidelity of different assemblers in metagenomic studies demonstrating that even under the simplest compositions the number of chimeric contigs involving different species is noticeable. We further showed that the assembly process reduces the accuracy of the functional classification of the metagenomicdataandthattheseerrorscanbeovercomeraisingthecoverageofthestudiedmetagenome.Theresults presented here highlight the particular difficulties that de novo genome assemblers face in multi-genome scenarios demonstrating that these difficulties, that often compromise the functional classification of the analyzed data, can be overcomewithahighsequencingeffort. Citation: Pignatelli M, Moya A (2011) Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data. PLoS ONE 6(5): e19984. doi:10.1371/journal.pone.0019984 Editor:JonathanH.Badger,J.CraigVenterInstitute,UnitedStatesofAmerica ReceivedDecember14,2010;AcceptedApril22,2011;PublishedMay23,2011 Copyright:?2011Pignatelli,Moya.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unr