ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.

Abstract

Paired-end sequencing resulting in gapped short reads is commonly used for de novo genome assembly. Assembly methods use paired-end sequences in a two-step process, first treating each read-end independently, only later invoking the pairing to join the contiguous assemblies (contigs) into gapped scaffolds. Here, we present ELOPER, a pre-processing tool for pair-end sequences that produces a better read library for assembly programs. ELOPER proceeds by simultaneously considering both ends of paired reads generating elongated reads. We show that ELOPER theoretically doubles read-lengths while halving the number of reads. We provide evidence that pre-processing read libraries using ELOPER leads to considerably improved assemblies as predicted from the Lander-Waterman model. http://sourceforge.net/projects/eloper Supplementary data are available at Bioinformatics online.