Clover: a clustering-oriented de novo assembler for Illumina sequences

BMC Bioinformatics
Ming-Feng HsiehChuan Yi Tang

Abstract

Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. In this paper, we develop a de Bruijn assembler, called Clover (clustering-oriented de novo assembler), that utilizes a novel k-mer clustering approach from the overlap-layout-consensus concept to deal with the sequencing errors generated by the Illumina platform. We further evaluate Clover's performance against several de Bruijn graph assemblers (ABySS, SOAPdenovo, SPAdes and Velvet), overlap-layout-consensus assemblers (Bambus2, CABOG and MSR-CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromosome 14). The results show that Clover achieves a superior assembly quality in terms of corrected N50 and E-size while remaining a significantly competitive in run time except SOAPdenovo. In addition, Clover was involved in the s...Continue Reading

References

Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Oct 28, 2008·Bioinformatics·Jason R MillerGranger Sutton
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Jun 10, 2010·Nature Reviews. Genetics·R David HawkinsBing Ren
Dec 1, 2010·Genome Biology·David R KelleySteven L Salzberg
Sep 20, 2011·Bioinformatics·Sergey KorenMihai Pop
Dec 8, 2011·Genome Research·Steven L SalzbergJames A Yorke
Dec 14, 2011·Genome Research·Jared T Simpson, Richard Durbin
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Dec 5, 2012·Journal of Bacteriology·Ming-Li LiouChuan Yi Tang
Aug 31, 2013·Bioinformatics·Aleksey V ZiminJames A Yorke

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP003856
ALJX00000000
The

Methods Mentioned

BETA
SGA
PCR

Software Mentioned

SGA
CABOG
Velvet
cs
GAGE
Allpaths
fastq
MSR
Clover
LG

Related Concepts

Related Feeds

Acinetobacter Infections

Acinetobacter infections have become common in hospitalized patients, especially in the intensive care unit setting and are difficult to treat due to their propensity to develop antimicrobial drug resistance. Discover the latest research on Acinetobacter Infections here.