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1、ARTICLeSFull-lengthtranscriptomeassemblyfromRNA-SeqdatawithoutareferencegenomeManfredGGrabherr1,8,BrianJHaas1,8,MoranYassour1–3,8,JoshuaZLevin1,DawnAThompson1,IdoAmit1,XianAdiconis1,LinFan1,RaktimaRaychowdhury1,QiandongZeng1,ZehuaChen1,EvanMauceli1,NirHa
2、cohen1,AndreasGnirke1,NicholasRhind4,FedericadiPalma1,BruceWBirren1,ChadNusbaum1,KerstinLindblad-Toh1,5,NirFriedman2,6&AvivRegev1,3,7MassivelyparallelsequencingofcDNAhasenableddeepandefficientprobingoftranscriptomes.Currentapproachesfortranscriptreconstr
3、uctionfromsuchdataoftenrelyonaligningreadstoareferencegenome,andarethusunsuitableforsampleswithapartialormissingreferencegenome.HerewepresenttheTrinitymethodfordenovoassemblyoffull-lengthtranscriptsandevaluateitonsamplesfromfissionyeast,mouseandwhitefly,
4、whosereferencegenomeisnotyetavailable.ByefficientlyconstructingandanalyzingsetsofdeBruijngraphs,Trinityfullyreconstructsalargefractionoftranscripts,includingalternativelysplicedisoformsandtranscriptsfromrecentlyduplicatedgenes.Comparedwithotherdenovotran
5、scriptomeassemblers,Trinityrecoversmorefull-lengthtranscriptsacrossabroadrangeofexpressionlevels,withasensitivitysimilartomethodsthatrelyongenomealignments.Ourapproachprovidesaunifiedsolutionfortranscriptomereconstructioninanysample,especiallyintheabsenc
6、eofareferencegenome.RecentadvancesinmassivelyparallelcDNAsequencing(RNA-Seq)andthenmergesequenceswithoverlappingalignment,spanningspliceprovideacost-effectivewaytoobtainlargeamountsoftranscriptomejunctionswithreadsandpaired-ends.Assembly-first(denovo)met
7、h-datafrommanyorganismsandtissuetypes1,2.Inprinciple,suchdatacanods,suchasABySS1,SOAPdenovo6orOases(E.Birney,Europeanallowustoidentifyallexpressedtranscripts3,ascompleteandcontigu-BioinformaticsInstitute,personalcommunication),usethereadstoousmRNAsequenc
8、efromthetranscriptionstartsitetothetranscriptionassembletranscriptsdirectly,whichcanbemappedsubsequentlytoaend,formultiplealternativelysplicedisoforms.However,reconstructionreferencegenome,ifavailable.Mapping-firstapproach
