Calling SNPs without a reference sequence |
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Authors: | Aakrosh Ratan Yu Zhang Vanessa M Hayes Stephan C Schuster Webb Miller |
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Institution: | (1) Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA;(2) Children's Cancer Institute Australia for Medical Research, University of New South Wales, Randwick, Australia |
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Abstract: | Background The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome
of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify
genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms
capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has
been reported on how to use these technologies to determine genetic differences among individuals of a species for which a
reference sequence is not available, which drastically limits the number of species that can easily benefit from these new
technologies. |
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Keywords: | |
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