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Plantagora Modeling Whole Genome Sequencing and Assembly of Plant Genomes 英文参考文献
Plantagora:ModelingWholeGenomeSequencingand
AssemblyofPlantGenomes
RogerBarthelson1*,AdamJ.McFarlin2,StevenD.Rounsley3,SarahYoung4
1iPlantCollaborative,TheBIO5Institute,UniversityofArizona,Tucson,Arizona,UnitedStatesofAmerica,2AppleInc.,Cupertino,California,UnitedStatesofAmerica,
3TheBIO5InstituteandSchoolofPlantSciences,UniversityofArizona,Tucson,Arizona,UnitedStatesofAmerica,4BroadInstitute,Cambridge,Massachusetts,United
StatesofAmerica
Abstract
Background: Genomics studies are being revolutionized by the next generation sequencing technologies, which have
madewholegenomesequencingmuchmoreaccessibletotheaverageresearcher.Wholegenomesequencingwiththe
newtechnologiesisadevelopingartthat,despitethelargevolumesofdatathatcanbeproduced,maystillfailtoprovidea
clearandthoroughmapofagenome.ThePlantagoraprojectwasconceivedtoaddressspecificallythegapbetweenhaving
thetechnicaltoolsforgenomesequencingandknowingpreciselythebestwaytousethem.
Methodology/Principal Findings: For Plantagora, a platform was created for generating simulated reads from several
differentplantgenomesofdifferentsizes.Theresultingreadfilesmimickedeither454orIlluminareads,withvaryingpaired
endspacing.Thousandsofdatasetsofreadswerecreated,mostderivedfromourprimarymodelgenome,ricechromosome
one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the
resultingassemblieswereevaluatedbyanextensivebatteryofmetricschosenforthesestudies.Themetricsincludedboth
statisticsoftheassemblysequencesandfidelity-relatedmeasuresderivedbyalignmentoftheassembliestotheoriginal
genomesourceforthereads.Theresultswerepresentedinawebsite,whichincludesadatagraphingtool,allcreatedto
help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to
testinganapproachinthelab.Someofourownconclusionsregardingthedifferentstrategieswerealsorecordedonthe
website.
Conclusions/Significance: Plantagora provides a substantial body of
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