CloG: A pipeline for closing gaps in a draft assembly using short reads

Abstract

Closing of gaps in draft assemblies using Next Generation Sequencing (NGS) data is becoming increasingly important. In this paper we present CloG, a software pipeline that uses NGS data to close gaps in draft assemblies. Firstly, CloG uses the VELVET assembler to generate a hybrid assembly from a mixture of reads: short reads from the NGS data and the original draft assembly (treated as long reads). It then closes gaps between adjacent contigs by reconciling (i.e., “stitching”) the two assemblies. By exploiting the strengths of both hybrid assembly and stitching reassembly, CloG is able to outperform its contemporaries in closing gaps in the draft assembly of the bacterium Burkholderia dolosa.