ESSENTIALS Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data 英文参考文献.docVIP

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ESSENTIALS Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data 英文参考文献.doc

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ESSENTIALS Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data 英文参考文献

ESSENTIALS:SoftwareforRapidAnalysisofHigh ThroughputTransposonInsertionSequencingData AldertZomer1,2*,PeterBurghout1,HesterJ.Bootsma1,PeterW.M.Hermans1,SachaA.F.T.van Hijum2,3,4,5 1Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands, 2Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, TheNetherlands, 3NIZO Food Research,Kluyver Centre for Genomics of IndustrialFermentation,Ede,TheNetherlands,4TIFoodandNutrition,Wageningen,TheNetherlands,5NetherlandsBioinformaticsCentre,Nijmegen,TheNetherlands Abstract High-throughputanalysisofgenome-widerandomtransposonmutantlibrariesisapowerfultoolfor(conditional)essential genediscovery.Recently,severalnext-generationsequencingapproaches,e.g.Tn-seq/INseq,HITSandTraDIS,havebeen developedthataccuratelymapthesiteoftransposoninsertionsbymutant-specificamplificationandsequencereadoutof DNAflankingthetransposoninsertionssite,assigningameasureofessentialitybasedonthenumberofreadsperinsertion siteflankingsequenceorpergene.However,analysisoftheselargeandcomplexdatasetsishamperedbythelackofan easytouseandautomatedtoolfortransposoninsertionsequencingdata.Tofillthisgap,wedevelopedESSENTIALS,an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalizationmethods,genomiclocationbiascorrection,datapreprocessingsteps,appropriatestatisticaltestsandvarious visualizationstoexaminetheresults,whilerequiringonlyaminimumofinputandhands-onworkfromtheresearcher.We successfullyappliedESSENTIALStoin-houseandpublishedTn-seq,TraDISandHITSdatasetsandweshowthatthevarious pre-andpost-processingstepsonthesequencereadsandcountdatawithESSENTIALSconsiderablyimprovethesensitivity andspecificityofpredictedgeneessentiality. Citation:ZomerA,Bu