將成對序列延伸成長序列改善組裝結構

Conversion of Mate-Pair Reads into Long Sequences for Improving Assembly Scaffolding

李昭宏(CHAO-HUNG LEE)

指導教授 ： 黃耀廷

國立中正大學/工學院/資訊工程學系/碩士(2016年)

摘要

利用成對序列(Mate Pair)來改善基因體組裝(Genome Assembly)之完整度已行之有年。雖然成對序列定序有著低價格優勢，其定序時品質並不穩定，且經常有汙染之情形。隨著第三代定序技術問世，其特有之長序列能有效地改善基因體組裝完整度。然而其缺點則是定序錯誤較多且價格高昂。因此本篇論文欲將成本相對較低的成對序列，利用計算方法轉變為長序列，以期能利用長序列的優點來改善基因體組裝。我們利用幾組真實測試資料來驗證我們方法的正確性與準確性。此外，我們也利用原始成對序列、由成對序列轉成的長序列，以及混合兩者分別對基因體組裝結果進行比較。

關鍵字

基因體組裝(Genome Assembly) ； 成對序列(Mate Pair) ； 次世代定序(Next Generation Sequencing)

並列摘要

Mate-pair scaffolding has been used from the early days of genome sequencing to improve the final assembly. Although the mate-pair sequencing is now affordable, its power and accuracy has be limited by the lower quality and contamination. The 3rd generation sequencing, which generates long reads,is helpful for accurate scaffolding. However, the error rates and cost of this technology are still too high. This thesis aims to convert low-cost mate-pair reads into long reads using computational approaches, which has the benefits of both mate-pair reads and long reads for scaffolding. We test our methods by using several real datasets and validate the accuracy of converted long reads. In addition, the scaffolding results are compared using mate-pair reads, long reads, and mixture of both material.

並列關鍵字

Next Generation Sequencing ； Genome Assembly ； Mate Pair

參考文獻

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