File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

TitleCOPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
Authors
Issue Date2012
Citation
Bioinformatics, 2012, v. 28 n. 22, p. 2870-2874 How to Cite?
AbstractMotivation: 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.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 30à 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. © 2012 The Author.
Persistent Identifierhttp://hdl.handle.net/10722/190306
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643

 

DC FieldValueLanguage
dc.contributor.authorLiu, Ben_US
dc.contributor.authorYuan, Jen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorLi, Zen_US
dc.contributor.authorXie, Yen_US
dc.contributor.authorChen, Yen_US
dc.contributor.authorShi, Yen_US
dc.contributor.authorZhang, Hen_US
dc.contributor.authorLi, Yen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorLuo, Ren_US
dc.date.accessioned2013-09-17T15:18:28Z-
dc.date.available2013-09-17T15:18:28Z-
dc.date.issued2012en_US
dc.identifier.citationBioinformatics, 2012, v. 28 n. 22, p. 2870-2874en_US
dc.identifier.issn1367-4803-
dc.identifier.urihttp://hdl.handle.net/10722/190306-
dc.description.abstractMotivation: 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.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 30à 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. © 2012 The Author.-
dc.languageengen_US
dc.relation.ispartofBioinformaticsen_US
dc.titleCOPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assemblyen_US
dc.typeArticleen_US
dc.identifier.emailLiu, B: bhliu@hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_US
dc.identifier.emailLuo, R: rbluo@hku.hken_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.identifier.doi10.1093/bioinformatics/bts563-
dc.identifier.pmid23044551-
dc.identifier.scopuseid_2-s2.0-84869401941-
dc.identifier.hkuros222160en_US
dc.identifier.volume28en_US
dc.identifier.issue22en_US
dc.identifier.spage2870en_US
dc.identifier.epage2874en_US

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats