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研究生:謝汶甫
研究生(外文):Hsieh, Wen-Fu
論文名稱:適用單端與雙端次世代定序之全自動智慧配接器偵測演算法
論文名稱(外文):Fully automatic intelligent adapter detection and trimming algorithm for single and paired-end NGS reads
指導教授:洪瑞鴻洪瑞鴻引用關係
指導教授(外文):Hung, Jui-Hung
口試委員:鐘育志林勇欣
口試委員(外文):Jong, Yuh-JyhLin, Yeong-Shin
口試日期:2017-08-29
學位類別:碩士
校院名稱:國立交通大學
系所名稱:生物資訊及系統生物研究所
學門:生命科學學門
學類:生物訊息學類
論文種類:學術論文
論文出版年:2017
畢業學年度:106
語文別:中文
論文頁數:39
中文關鍵詞:次世代定序配接器
外文關鍵詞:Next-Generation Sequencingadapter
相關次數:
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目錄摘要-----------------------------------------------------------------------------------i
ABSTRACT----------------------------------------------------------------------------ii
致謝-----------------------------------------------------------------------------------iii
目錄---------------------------------------------------------------------------------------------iv
圖目錄-------------------------------------------------------------------------------------------vii
表目錄--------------------------------------------------------------------------------------------ix
一、 簡介-------------------------------------------------------------------------------------1
1-1基因序列----------------------------------------------------------------------------------1
1-1-1去氧核醣核酸(DNA) ---------------------------------------------------------------1
1-1-2核糖核酸(RNA) ---------------------------------------------------------------------2
1-2次世代定序(Next-Generation Sequencing, NGS) -------------------------------------------3
1-3 配接器污染的影響--------------------------------------------------------------------------6
1-4定序實驗-----------------------------------------------------------------------------------7
1-4-1染色質免疫沈澱定序(Chromatin Immunoprecipitation, ChIP-seq) ----------------------7
1-4-2全轉錄體霰彈槍定序(RNA Sequencing, RNA-seq) --------------------------------------8
1-4-3微小RNA定序(small RNA-seq) -----------------------------------------------------9
1-4-4 Assay for Transposase - Accessible Chromatin with highthroughput (ATAC-seq)---------- 10
二、 相關研究---------------------------------------------------------------------------------11
2-1 PEAT------------------------------------------------------------------------------------11
2-2 Skewer -----------------------------------------------------------------------------------13
2-3 AdapterRemoval_v2--------------------------------------------------------------------------14
2-4 DNApi---------------------------------------------------------------------------------------14
三、 動機與目標------------------------------------------------------------------------------16
3-1研究動機------------------------------------------------------------------------------------16
3-2研究目標------------------------------------------------------------------------------------16
四、 研究方法---------------------------------------------------------------------------------17
4-1單端配接器偵測流程------------------------------------------------------------------------17
4-1-1比對回基因體------------------------------------------------------------------------18
4-1-2取得候選配接器----------------------------------------------------------------------20
4-1-3配接器組裝------------------------------------------------------------------------21
4-2 雙端配接器偵測流程----------------------------------------------------------------------23
4-2-1平行化資料取得與資料比對(Multi threads)------------------------------------------23
4-2-2優化資料比對效能(SIMD)-----------------------------------------------------------24
4-2-3內存記憶體優化(Tcmalloc)----------------------------------------------------------25
五、 研究結果--------------------------------------------------------------------------------26
5-1資料測試-----------------------------------------------------------------------------------26
5-2效能比較-----------------------------------------------------------------------------------32
六、 討論--------------------------------------------------------------------------------------34
6-1單端配接器自動偵測演算法---------------------------------------------------------------34
6-2雙端配接器自動偵測演算法---------------------------------------------------------------34
七、 結論--------------------------------------------------------------------------------------35
參考資料--------------------------------------------------------------------------------------36
自傳--------------------------------------------------------------------------------------------39
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