File Download
There are no files associated with this item.
Links for fulltext
(May Require Subscription)
- Publisher Website: 10.1093/bioinformatics/bts563
- Scopus: eid_2-s2.0-84869401941
- PMID: 23044551
- WOS: WOS:000311303500002
- Find via
Supplementary
- Citations:
- Appears in Collections:
Article: COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
Title | COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly |
---|---|
Authors | |
Issue Date | 2012 |
Citation | Bioinformatics, 2012, v. 28 n. 22, p. 2870-2874 How to Cite? |
Abstract | 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⠲ 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 Identifier | http://hdl.handle.net/10722/190306 |
ISSN | 2023 Impact Factor: 4.4 2023 SCImago Journal Rankings: 2.574 |
ISI Accession Number ID |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Liu, B | en_US |
dc.contributor.author | Yuan, J | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.contributor.author | Li, Z | en_US |
dc.contributor.author | Xie, Y | en_US |
dc.contributor.author | Chen, Y | en_US |
dc.contributor.author | Shi, Y | en_US |
dc.contributor.author | Zhang, H | en_US |
dc.contributor.author | Li, Y | en_US |
dc.contributor.author | Lam, TW | en_US |
dc.contributor.author | Luo, R | en_US |
dc.date.accessioned | 2013-09-17T15:18:28Z | - |
dc.date.available | 2013-09-17T15:18:28Z | - |
dc.date.issued | 2012 | en_US |
dc.identifier.citation | Bioinformatics, 2012, v. 28 n. 22, p. 2870-2874 | en_US |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://hdl.handle.net/10722/190306 | - |
dc.description.abstract | 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⠲ 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.language | eng | en_US |
dc.relation.ispartof | Bioinformatics | en_US |
dc.title | COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly | en_US |
dc.type | Article | en_US |
dc.identifier.email | Liu, B: bhliu@hku.hk | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.email | Lam, TW: hresltk@hkucc.hku.hk | en_US |
dc.identifier.email | Luo, R: rbluo@hku.hk | en_US |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.authority | Lam, TW=rp00135 | en_US |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.doi | 10.1093/bioinformatics/bts563 | - |
dc.identifier.pmid | 23044551 | - |
dc.identifier.scopus | eid_2-s2.0-84869401941 | - |
dc.identifier.hkuros | 222160 | en_US |
dc.identifier.volume | 28 | en_US |
dc.identifier.issue | 22 | en_US |
dc.identifier.spage | 2870 | en_US |
dc.identifier.epage | 2874 | en_US |
dc.identifier.isi | WOS:000311303500002 | - |
dc.identifier.issnl | 1367-4803 | - |