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Plant Biotechnol J. 2009 May;7(4):312-7. doi: 10.1111/j.1467-7652.2009.00406.x.

Discovering genetic polymorphisms in next-generation sequencing data.

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Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.


The ongoing revolution in DNA sequencing technology now enables the reading of thousands of millions of nucleotide bases in a single instrument run. However, this data quantity is often compromised by poor confidence in the read quality. The identification of genetic polymorphisms from this data is therefore problematic and, combined with the vast quantity of data, poses a major bioinformatics challenge. However, once these difficulties have been addressed, next-generation sequencing will offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems. We describe the recent advances in next-generation sequencing technology, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species.

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