SNP Discovery through Next-Generation Sequencing and Its Applications

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dc.contributor.authorKumar, Santosh
dc.contributor.authorBanks, Travis W.
dc.contributor.authorCloutier, Sylvie
dc.date.accessioned2015-05-14T16:38:58Z
dc.date.available2015-05-14T16:38:58Z
dc.date.issued2012-11-22
dc.date.updated2015-03-29T13:33:48Z
dc.description.abstractThe decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
dc.description.versionPeer Reviewed
dc.identifier.citationSantosh Kumar, Travis W. Banks, and Sylvie Cloutier, “SNP Discovery through Next-Generation Sequencing and Its Applications,” International Journal of Plant Genomics, vol. 2012, Article ID 831460, 15 pages, 2012. doi:10.1155/2012/831460
dc.identifier.urihttp://dx.doi.org/10.1155/2012/831460
dc.identifier.urihttp://hdl.handle.net/1993/30505
dc.language.rfc3066en
dc.rightsopen accessen_US
dc.rights.holderCopyright © 2012 Santosh Kumar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.titleSNP Discovery through Next-Generation Sequencing and Its Applications
dc.typeJournal Article
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