Calling SNPs without a reference sequence

BMC Bioinformatics

Software

Stephan C Schuster¹  Yu Zhang¹  Webb Miller¹  Aakrosh Ratan¹  Vanessa M Hayes² 

[1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA;Children's Cancer Institute Australia for Medical Research, University of New South Wales, Randwick, Australia;

关键词: Dial;    Duplicate Region;    Read Coverage;    Human Reference Genome;    Genotyping Array;   

DOI  :  10.1186/1471-2105-11-130

 received in 2009-08-31, accepted in 2010-03-15,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences.ConclusionsDIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/.

【 授权许可】

CC BY   
© Ratan et al; licensee BioMed Central Ltd. 2010