COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.
Bioinformatics
; 28(22): 2870-4, 2012 Nov 15.
Article
em En
| MEDLINE
| ID: mdl-23044551
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
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Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Mapeamento Cromossômico
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Análise de Sequência de DNA
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Arabidopsis
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Genômica
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article