{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T06:18:56Z","timestamp":1774937936816,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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\u2032 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.<\/jats:p>\n               <jats:p>Result: 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\u00d7 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.<\/jats:p>\n               <jats:p>Availability and implementation: COPE is implemented in C++ and is freely available as open-source code at ftp:\/\/ftp.genomics.org.cn\/pub\/cope.<\/jats:p>\n               <jats:p>Contact: \u00a0twlam@cs.hku.hk or luoruibang@genomics.org.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts563","type":"journal-article","created":{"date-parts":[[2012,10,9]],"date-time":"2012-10-09T00:42:28Z","timestamp":1349743348000},"page":"2870-2874","source":"Crossref","is-referenced-by-count":134,"title":["COPE: an accurate <i>k<\/i>-mer-based pair-end reads connection tool to facilitate genome assembly"],"prefix":"10.1093","volume":"28","author":[{"given":"Binghang","family":"Liu","sequence":"first","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Jianying","family":"Yuan","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Siu-Ming","family":"Yiu","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Zhenyu","family":"Li","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Yinlong","family":"Xie","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Yanxiang","family":"Chen","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Yujian","family":"Shi","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]},{"given":"Ruibang","family":"Luo","sequence":"additional","affiliation":[{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"},{"name":"1 HKU-BGI BAL (Bioinformatics Algorithms and Core Technology Research Laboratory), The University of Hong Kong, Hong Kong, 2BGI-Shenzhen, Shenzhen, Guangdong 518083, China and 3Department of Computer Science, The University of Hong Kong, Hong Kong"}]}],"member":"286","published-online":{"date-parts":[[2012,10,8]]},"reference":[{"key":"2023012513145552300_bts563-B1","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1111\/j.1755-0998.2011.03024.x","article-title":"Field guide to next-generation DNA 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