Clover: a clustering-oriented de novo assembler for Illumina sequences
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SOFTWARE
Clover: a clustering‑oriented de novo assembler for Illumina sequences Ming‑Feng Hsieh1, Chin Lung Lu1 and Chuan Yi Tang1,2* *Correspondence: [email protected] 1 Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan Full list of author information is available at the end of the article
Abstract Background: 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 sequenc‑ ing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. Results: In this paper, we develop a de Bruijn assembler, called Clover (clusteringoriented 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-con‑ sensus assemblers (Bambus2, CABOG and MSR-CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromo‑ some 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 sequencing projects of bacterial genomes Acinetobacter baumannii TYTH-1 and Morganella morganii KT. Conclusions: The marvel clustering-based approach of Clover that integrates the flexibility of the overlap-layout-consensus approach and the efficiency of the de Bruijn graph method has high potential on de novo assembly. Now, Clover is freely available as open source software from https://oz.nthu.edu.tw/~d9562563/src.html. Keywords: De novo genome assembly, DNA sequencing, De bruijn graph
Background Massively parallel DNA sequencing has become a prominent tool in biological research [1, 2]. The high-throughput and low cost of next-generation sequencing technologies produce high coverage of reads. The Illumina platform is one of the most commonly used sequencers, producing reads with lengths ranging from 35 to 300 bp. The de Bruijn graph approach is prevalent in the de novo assembly using Illumina reads, and it constitutes all possible substrings of length k (termed k-mers) from the reads to efficiently process the huge sequencing data. Choosing the length of k is an important issue in the de Bruijn graph approach. Theoretically, for reads without sequence errors, smaller k-mers © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropri
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