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Bioinformatics. 2012 Nov 15;28(22):2870-4. doi: 10.1093/bioinformatics/bts563. Epub 2012 Oct 8.

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

Author information

1
HKU-BGI BAL-Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong.

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 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.

AVAILABILITY AND IMPLEMENTATION:

COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope.

CONTACT:

twlam@cs.hku.hk or luoruibang@genomics.org.cn

PMID:
23044551
DOI:
10.1093/bioinformatics/bts563
[Indexed for MEDLINE]

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