次世代定序技術藉由低成本且高通量的 reads 來改進基因體學，而這個改變促進了近期組序軟體的發展。許多基於 de Bruijn graph 的組序方法被證實對於 Illumina reads 來說很有效率。然而，定序機產生的序列錯誤使得組序的分析變得複雜且影響了下游基因體學研究的品質。
在這篇論文中，我們發展了一個基於 de Bruijn 的組序軟體，稱它為 Clover （叢集導向組序軟體），它利用一個從 overlap-layout-consensus 概念中獲得的新穎 k-mer 叢集方法來處理 Illumina 平台產生的序列錯誤。我們進一步使用三組資料（Staphylococcus aureus，Rhodobacter sphaeroides 和人類第十四號染色體）來評估 Clover 相對於數個 de Bruijn graph 組序軟體（ABySS，SOAPdenovo，SPAdes 與 Velvet）， overlap-layout-consensus 組序軟體（Bambus2，CABOG 與 MSR-CA）與 string graph 組序軟體（SGA）的表現。其結果顯示 Clover 在驗證後的 N50 與 E-size 的項目中獲得較高的組序品質，同時保持在執行速度上的競爭性（除了 SOAPdenovo）。
這個新穎的叢集導向方法， Clover ，整合了 overlap-layout-consensus 方法的彈性與 de Bruijn graph 方法的效率，在組序上有很高的潛力。現在， Clover 可以從 http://oz.nthu.edu.tw/~d9562563/ 免費下載。

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 thesis, 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.
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 at http://oz.nthu.edu.tw/~d9562563/.

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