Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis.

ABSTRACT: The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to obtain a high SNP recovery and low false discovery rate but are not designed to account appropriately the frequency of the variants. Instead, algorithms designed to account for the frequency of SNPs give precise results for estimating the levels and the patterns of variability. These algorithms are focused on the unbiased estimation of the variability and not on the high recovery of SNPs. Here, we impl

SUBMITTER: Navarro J 

PROVIDER: S-EPMC5582667 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature