Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets

Genomics

Arndt von Haeseler¹  Prabhavathi Talloji¹  Fritz Joachim Sedlazeck¹  Andreas Bachmair¹ 

关键词: Next generation sequencing;    Read alignment;    SNP validation;    SNP calling;    Sub-genomic library;   

DOI  :  10.1016/j.ygeno.2012.12.001

学科分类：医学（综合）

来源: Academic Press

【 摘 要 】

Identificationofsinglenucleotidepolymorphisms(SNPs)isakeyelementinsequence-basedgeneticanalysis.Nextgenerationsequencingoffersacost-effectivebasistogeneratethenecessary,largesequencedatasets,andbioinformaticmethodsarebeingdevelopedtoprocesssequencingmachinereadouts.WewereinterestedindetectionofSNPsina350#xA0;kbregionofanEMS-mutagenizedArabidopsischromosome3.TheregionwasselectivelyanalyzedusingPCR-generated,overlappingfragmentsforSolexasequencing.Theensuingreadsprovidedahighcoverageandwereprocessedbioinformatically.InordertoassesstheSNPcandidatesobtainedwithafrequentlyusedalignmentprogramandSNPcaller,wedevelopedanadditionalmethodthatallowstheidentificationofhighconfidenceSNPloci.Themethodcaneasilybeappliedtocompletegenomesequencedataofsufficientcoverage.

【 授权许可】

Unknown   

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