title: COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.
abstract: BACKGROUND
  The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3' ends of each read pair, one is able to construct longer reads for assembling. However, effectively joining two overlapped pair-end reads remains a challenging task.
  
  
  RESULTS
  In this article, we present an efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.
  
  
  METHODS
  COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope.
  
  
  BACKGROUND
  twlam@cs.hku.hk or luoruibang@genomics.org.cn
authors.affiliation: HKU-BGI BAL-Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong.
authors.forename: Binghang
authors.initials: B
authors.lastname: Liu
authors.forename: Jianying
authors.initials: J
authors.lastname: Yuan
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Li
authors.forename: Yinlong
authors.initials: Y
authors.lastname: Xie
authors.forename: Yanxiang
authors.initials: Y
authors.lastname: Chen
authors.forename: Yujian
authors.initials: Y
authors.lastname: Shi
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D020451:Contig Mapping; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*