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1、REVIEWSSTUDYDESIGNSNext-generationtranscriptomeassemblyJeffreyA. MartinandZhongWangAbstract
2、Transcriptomicsstudiesoftenrelyonpartialreferencetranscriptomesthatfailtocapturethefullcatalogueoftranscriptsandtheirvariations.Recentadvancesinsequencingtechnologiesandassemblyalgorith
3、mshavefacilitatedthereconstructionoftheentiretranscriptomebydeepRNAsequencing(RNA-seq),evenwithoutareferencegenome.However,transcriptomeassemblyfrombillionsofRNA-seqreads,whichareoftenveryshort,posesasignificantinformaticschallenge.ThisReviewsummarizestherecentdevelopmentsintr
4、anscriptomeassemblyapproaches—reference-based,de novoandcombinedstrategies—alongwithsomeperspectivesontranscriptomeassemblyinthenearfuture.Identifyingthefullsetoftranscripts—includinglargeReconstructingacomprehensivetranscriptomefromRNAsequencing(RNA-seq).Anexperimentalandsmal
5、lRNAs,noveltranscriptsfromunannotatedshortreadshasmanyinformaticschallenges.Similarprotocolthatusesnext-genes,splicingisoformsandgene-fusiontranscripts—toshort-readgenomeassembly,transcriptomeassemblygenerationsequencingservesasthefoundationforacomprehensivestudyofinvolvespiec
6、ingtogethershort,low-qualityreads.Typicaltechnologiestosequencethetranscriptome.Foralongtime,ourknowledgeNGSdatasetsareverylarge(severalgigabasestotera-theRNAmoleculeswithinaofthetranscriptomewaslargelyderivedfromgenebases),whichrequirescomputingsystemstohavelargebiologicalsam
7、pleinanefforttodeterminetheprimarypredictionsandlimitedESTevidenceandhasthere-memoriesand/ormanycorestorunparallelalgorithms.sequenceandrelativeforebeenpartialandbiased.Recently,however,whole-Severalshort-readassemblershavebeendevelopedtoabundanceofeachRNA.transcriptomesequenc
8、ingusingnext-generationtacklethesechallenges6–9,includingVelvet6,ABYSS7andsequencing(NGS)technologies,orRNAsequencingALLPATHS8.Althoughthesetoolshaveachievedreason-Sequencingdepth(RNA-seq),hasstartedtorevealthecomplexlandscapeablesuccessintheassemblyofgenomes9,10,theycannotThe
9、averagenumberofreadsrepresentingagivennucleotideanddynamicsof
