title: ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  BACKGROUND
  http://sourceforge.net/projects/eloper
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
authors.forename: David H
authors.initials: DH
authors.lastname: Silver
authors.forename: Shay
authors.initials: S
authors.lastname: Ben-Elazar
authors.forename: Alexei
authors.initials: A
authors.lastname: Bogoslavsky
authors.forename: Itai
authors.initials: I
authors.lastname: Yanai
mesh_terms: D020451:Contig Mapping; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software