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

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Rallapalli, Ghanasyam, Corredor-Moreno, Pilar, Chalstrey, Edward, Page, Martin and Maclean, Daniel (2019) Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence. BMC Bioinformatics, 20. ISSN 1471-2105

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Abstract

Background Traditional 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. Results We 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. Conclusions CHERIPIC 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.

Item Type: Article
Uncontrolled Keywords: bulk segregant analysis,mapping by sequencing,next generation mapping,structural biology,biochemistry,molecular biology,computer science applications,applied mathematics ,/dk/atira/pure/subjectarea/asjc/1300/1315
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Computing Sciences
Faculty of Science > School of Biological Sciences
Faculty of Science > The Sainsbury Laboratory
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 18 Jan 2019 13:30
Last Modified: 21 Oct 2022 21:34
URI: https://ueaeprints.uea.ac.uk/id/eprint/69614
DOI: 10.1186/s12859-018-2515-5

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