A Re-sequencing Tool For Next Generation Sequencing Based On Burrows-Wheeler Transform

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研究生：	盧振華 Lu, Chen-Hua
論文名稱：	A Re-sequencing Tool For Next Generation Sequencing Based On Burrows-Wheeler Transform 基於Burrows-Wheeler轉換之次世代定序技術重定序工具
指導教授：	唐傳義 Tang, Chuan-Yi
口試委員:
學位類別：	碩士 Master
系所名稱：	電機資訊學院 - 資訊工程學系 Computer Science
論文出版年：	2010
畢業學年度：	98
語文別：	英文
論文頁數：	39
中文關鍵詞：	NGS 、BWT 、FM-index 、重定序、短序列讀數、去氧核醣核酸
外文關鍵詞：	NGS, BWT, FM-index, re-sequencing, short read, DNA
相關次數：	點閱：1 下載：0
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本篇論文中，我們呈現了一個適用於次世代定序技術資料的重定序工具。這些資料是由大量的短序列所構成的，並將被對應到一個參考基因體上。我們修改並實作了Borrows-Wheeler Transform與FM-index的演算法，以此對人類的基因體建立索引；並提出了一個分割短序列的方法，使我們在對應時得以容許更長的漢明距離。最後，我們從1000 Genome Project中選出4組不同長度的真實資料，在個人電腦上進行測試，藉此展現此工具的性能，並與bowtie這個廣為使用的工具進行比較。

In this thesis, we present a re-sequencing tool designed for the Next Generation Sequencing (NGS) data. These data are composed huge amount of short reads, which are to align onto a referenced genome. We modified and implemented the algorithm of Borrows-Wheeler Transform and FM-index to build the genome index of human, and proposed an idea to segment each short read which lead us to align short reads with longer Hamming distance. Finally, we used 4 real data sets with different lengths form 1000 Genome Project to demonstrate the performance of our tool with a personal computer, and compared the results with a widely used tool, bowtie.

中文摘要 ............................................................................................................................ iii
ABSTRACT ....................................................................................................................... iv
ACKNOWLDGEMENTS ................................................................................................. v
TABLE OF CONTENTS .................................................................................................. vi
Chapter 1 - Introduction ................................................................................................... 1
Chapter 2 - Material and Methods ................................................................................... 4
2.1. Problem Definition ...................................................................................... 4
2.2. Material ....................................................................................................... 5
2.3. Store DNA Base in Binary Format ............................................................. 6
2.4. Un-aligned Memory Access and Limitation ............................................... 7
2.5. Burrows-Wheeler Transform ...................................................................... 8
2.6. FM-index ................................................................................................... 10
2.7. Building Index from Genome ................................................................... 16
2.8. Matching Reads with Seeds ...................................................................... 20
2.9. Aligning Reads by Checking Hamming Distance .................................... 22
2.10. Parallelization in Multi-thread Programming ........................................... 23
Chapter 3 - Result and Discussion .................................................................................. 26
3.1. Building Index from Genome ................................................................... 26
3.2. Read alignment ......................................................................................... 27
Chapter 4 - Conclusion and Future Work ..................................................................... 35
4.1 Conclusion ................................................................................................ 35
4.2 Future Work .............................................................................................. 36
REFERENCES ................................................................................................................. 38

                                

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12. NCBI Human Genome Resources. http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/
13. 1000 Genomes Project. http://www.1000genomes.org/

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