Evaluation of genome scaffolding tools using pooled clone sequencing

Abstract

DNA sequencing technologies hold great promise in generating information that will guide scientists to understand howthe genome affects human health and organismal evolution. The process of generating raw genome sequence data becomes cheaperand faster, but more error-prone. Assembly of such data into high-quality finished genome sequences remains challenging. Manygenome assembly tools are available, but they differ in terms of their performance and their final output. More importantly, it remainslargely unclear how to best assess the quality of assembled genome sequences. Here we evaluate the accuracies of several genomescaffolding algorithms using two different types of data generated from the genome of the same human individual: whole genomeshotgun sequencing (WGS) and pooled clone sequencing (PCS). We observe that it is possible to obtain better assemblies if PCS dataare used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-awarescaffolding algorithms remain an open problem.