Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.

ABSTRACT: Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling

SUBMITTER: Song K 

PROVIDER: S-EPMC5071758 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature