SNP markers retrieval for a non-model species: a practical approach.

ABSTRACT:

Background

SNP (Single Nucleotide Polymorphism) markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC) on 454 data from four lily genotypes and compared results with respect to SNP retrieval.

Results

CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter aver

SUBMITTER: Shahin A 

PROVIDER: S-EPMC3298514 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature