Calling SNPs without a reference sequence

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. Results: We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying singlebase substitutions between two closely related genomes without the help of a reference genome. The metho...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes, Stephan C. Schuster, Webb Miller
• Keywords: BMCBI 2010, Genetic Differences, Genome, Reference Genome