基因定序(genome sequencing)是研究基因體非常重要的項目，目前已有許多第二代基因定序(next-generation sequencing, NGS)技術，例如Roche/454 pyrosequencing、Illmina Genome Analyzer (IGA)、Helicos以及ABI SOLiD等，因為其低成本與高輸出產量的特性，被廣泛應用在許多基因體定序計畫之中。然而，第二代基因定序技術產生的序列資料往往包含很多錯誤，使得後續的組序(genome assembly)工作變得更加困難。
過去的研究顯示可以透過結合兩種第二代基因定序技術的資料，交互比對來修正單一定序技術產生的錯誤。本篇論文提出一個組序流程，藉由結合454與IGA兩種定序技術的資料來提升組序的品質。本論文首先利用454的序列資料進行初步的組序工作，接著找出454組序中疑似有錯誤的部分，稱為「三元結構」，並且透過兩種運用比對IGA序列資料的分析方法來解決454組序中的模糊結構。我們使用兩個物種的基因體序列資料來驗證上述組序流程的正確性，實驗的結果顯示該流程可以有效偵測組序中的三元結構，並解決一半以上的三元結構。

Genome sequencing is the first step to study a new genome. Recent advance in next-generation sequencing (NGS) technologies, such as Roche/454 pyrosequencing, Illumina Genome Analyzer (IGA), Helicos and ABI SOLiD), enables high-throughput sequencing data with lower cost than conventional sequencing technologies such as Sanger. However, the sequencing data generated by NGS technologies usually contain many errors, making the following genome assembly relatively difficult.
Previous studies have revealed that these sequencing errors can be corrected via combining sequencing data from different NGS technologies. This study presents an assembly pipeline, which utilizes sequencing data from both 454 and IGA technologies to improve genome assembly. This pipeline first assembled 454 sequencing data to construct a preliminary assembly. Then, the connections with suspicious errors in the preliminary assembly, denoted triad structure, were identified by a detection algorithm and solved by two analyses using IGA sequencing data. We used two genomes to evaluate the proposed assembly pipeline. The experimental results show that our pipeline can detect the triad structures in the preliminary assemblies and solve more than half of them.

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