Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data A Simulation Approach 英文参考文献.docVIP

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Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data A Simulation Approach 英文参考文献.doc

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Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data A Simulation Approach 英文参考文献

EvaluatingCharacteristicsofDeNovoAssemblySoftware on454TranscriptomeData:ASimulationApproach MarvinMundry1,ErichBornberg-Bauer1,MichaelSammeth2,PhilineG.D.Feulner1* 1EvolutionaryBioinformatics,InstituteforEvolutionandBiodiversity,Westfaelische-Wilhelms-University,Muenster,Germany,2FunctionalBioinformatics,CentreNacional d’Ana`lisi Geno`mica(CNAG),Barcelona,Spain Abstract Background:Thequantityoftranscriptomedataisrapidlyincreasingfornon-modelorganisms.Assequencingtechnology advances,focusshiftstowardssolvingbioinformaticchallenges,ofwhichsequencereadassemblyisthefirsttask.Recent studieshavecomparedtheperformanceofdifferentsoftwaretoestablishabestpracticefortranscriptomeassembly.Here, weadaptedasimulationapproachtoevaluatespecificfeaturesofassemblyprogramson454data.Thenoveltyofourstudy isthatthesimulationallowsustocalculateamodelassemblyasreferencepointforcomparison. Findings: The simulation approach allows us to compare basic metrics of assemblies computed by different software applications(CAP3,MIRA,Newbler,andOases)toaknownoptimalsolution.WefoundMIRAandCAP3areconservativein mergingreads.Thisresultedincomparablyhighnumberofshortcontigs.Incontrast,Newblermorereadilymergedreads intolongercontigs,whileOasesproducedtheoverallshortestassembly.Duetothesimulationapproach,readscouldbe tracedbacktotheircorrectplacementwithinthetranscriptome.Togetherwithmappingreadsontotheassembledcontigs, wewereabletoevaluateambiguityintheassemblies.ThisanalysisfurthersupportedtheconservativenatureofMIRAand CAP3,whichresultedinlowproportionsofchimericcontigs,buthighredundancy.Newblerproducedlessredundancy,but theproportionofchimericcontigswashigher. Conclusion: Our evaluation of four assemblers suggested that MIRA and Newbler slightly outperformed the other programs, while showing contrasting characteristics. Oases did not perform very well on the 454 reads. Our evaluation indicated that the software was either conservative (MIRA) or liberal (Newbler) about merging reads into contigs. Thi