Pebble and Rock Band Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler 英文参考文献.docVIP

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Pebble and Rock Band Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler 英文参考文献.doc

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Pebble and Rock Band Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler 英文参考文献

PebbleandRockBand:HeuristicResolutionofRepeats andScaffoldingintheVelvetShort-ReaddeNovo Assembler DanielR.Zerbino1*,GayleK.McEwen2,ElliottH.Margulies2,EwanBirney1 1EuropeanBioinformaticsInstitute,WellcomeTrustGenomeCampus,Hinxton,Cambridge,UnitedKingdom,2GenomeTechnologyBranch,NationalHumanGenome ResearchInstitute,NationalInstitutesofHealth,Bethesda,Maryland,UnitedStatesofAmerica Abstract Background:Despitetheshortlengthoftheirreads,micro-readsequencingtechnologieshaveshowntheirusefulnessfor de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies. Principal Findings: We present a novel heuristic algorithm, Pebble, which uses paired-end read information to resolve repeatsandscaffoldcontigstoproducelarge-scaleassemblies.Insimulations,wecanachieveweightedmedianscaffold lengths(N50)ofabove1MbpinBacteriaandabove100kbpinmorecomplexorganisms.Usingrealdatasetsweobtaineda 96kbp N50 in Pseudomonas syringae and a unique 147kbp scaffold of a ferret BAC clone. We also present an efficient algorithmcalledRockBandfortheresolutionofrepeatsinthecaseofmixedlengthassemblies,wheredifferentsequencing platformsarecombinedtoobtainacost-effectiveassembly. Conclusions: These algorithms extend the utility of short read only assemblies into large complex genomes. They have beenimplementedandmadeavailablewithintheopen-sourceVelvetshort-readdenovoassembler. Citation:ZerbinoDR,McEwenGK,MarguliesEH,BirneyE(2009)PebbleandRockBand:HeuristicResolutionofRepeatsandScaffoldingintheVelvetShort-Read deNovoAssembler.PLoSONE4(12):e8407.doi:10.1371/journal.pone.0008407 Editor:StevenL.Salzberg,UniversityofMaryland,UnitedStatesofAmerica ReceivedSeptember4,2009;AcceptedOctober21,2009;PublishedDecember22,2009 Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsPublicDomaindeclarationwhichstipulatesthat,onceplacedinthepublic domain,thisworkmaybefreelyreproduced,distributed,transmitted,modified,builtupon,orotherwiseusedbyanyon