Exploring genome characteristics and sequence quality without a reference

摘要

Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many c7e novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.Availability: The software described is freely available online (https:// github.com/jts/sga) and open source under the GNU Public License.