Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence

BMC Bioinformatics

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[1] The Sainsbury Laboratory, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK;The Sainsbury Laboratory, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK;0000 0001 1092 7967, grid.8273.e, Norwich Medical School, University of East Anglia, James Watson Road, NR4 7UQ, Norwich, UK;The Sainsbury Laboratory, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK;0000 0001 2175 7246, grid.14830.3e, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK;The Sainsbury Laboratory, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK;0000 0001 2324 0507, grid.88379.3d, Birkbeck, University of London, Bloomsbury, WC1E 7HX, London, UK;

关键词: Mapping by sequencing;    Next generation mapping;    Bulk segregant analysis;   

DOI  :  10.1186/s12859-018-2515-5

来源: publisher

【 摘 要 】

BackgroundTraditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. High throughput sequencing based Mapping-by-sequencing approach requires an ordered genome assembly and cannot be used with fragmented, un-scaffolded draft genomes, limiting its application to model species and precluding many important organisms.ResultsWe addressed this gap in resource and presented a computational method and software implementations called CHERIPIC (Computing Homozygosity Enriched Regions In genomes to Prioritise Identification of Candidate variants). We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively.ConclusionsCHERIPIC allows users to rapidly analyse bulk segregant sequence data and we have made it available as a pre-packaged binary with all dependencies for Linux and MacOS and as Galaxy tool.

【 授权许可】

CC BY