SNP Assessment on Draft Genomes from Next Generation Sequencing Data
Michael Piechotta and Christoph Dieterich
from: Next-generation Sequencing: Current Technologies and Applications (Edited by: Jianping Xu). Caister Academic Press, U.K. (2014)
The number of genome projects has dramatically increased with the advent of high-throughput sequencing technologies. Typically, most assemblies remain in draft status. We present two methods for robust polymorphism detection on draft genomes. The first application, ACCUSA identifies true SNPs on draft genomes by considering the reference base call quality. We exemplify the advantages of ACCUSA by using publicly available sequencing data from yeast strains. Furthermore, we present a novel method ACCUSA2 that allows to identify SNPs between sequenced samples and show that ACCUSA2 outperforms a state of the art SNP caller in an in silico benchmark read more ...