臺灣博碩士論文加值系統

随著次世代定序技術的問世，它已經成為基因體研究中最重要的資料來源之一。與傳統的方法比較，次世代定序能在可行的時間與預算內，提供高通量的序列以及定量生物體活動的能力。然而，在獲取生物上有意義的結果之前，完成一個次世代定序的分析需要一系列命令列下運作工具的參與，以及龐大的計算資源，給予生物學家以及臨床人員很高的分析進入門檻，他們甚而無法解讀自己的序結資料。因此本研究提出了一個線上分析次世代定序平台，BioCloud，它得以自動化常見的定序分析流程，並且根據分析結果產生總覽報表。進一步，使用者能設計自訂的分析流程並擴充現有的流程實作來支援更多種類的定序與分析方法。藉由在 BioCloud 上分析次世代定序，研究者能以更互動式與方便的方式來了解他們的資料，並且讓整個分析更容易地重現。

With the advent of next-generation sequencing (NGS), it has become one of the most important data sources in genome-wide study. Compared with traditional methods, NGS provides high throughput sequencing reads and ability to quantify expression of biological activities in feasible range of time and budget. However, before obtaining biologically meaningful results, a NGS data analysis involves series of command-line tools to process and requires extensive computation resources, which imposes a high barrier for biologists and clinicians to enter NGS analysis and even interpret their own data. Therefore, in this study, an online NGS analysis platform, BioCloud, is proposed to automate common analysis pipelines and generate summary report based on the analysis results. Furthermore, users can design their custom analysis pipelines and extends the existed implementation to support a wider set of NGS sequencing types and analysis methods. By conducting NGS analyses on BioCloud, researchers can understand their data in a more interactive and convenient way and the analyses results can be easily reproducible.

口試委員會審定書.................................. i
誌謝.......................................... ii
摘要.......................................... iii
Abstract........................................ iv
Contents........................................ v
List of Figures..................................... viii
List of Tables ..................................... x
1 Introduction.................................... 1
1.1 Motivation.................................. 1
1.2 Specific aims................................ 2
1.3 Next-generation sequencing ........................ 3
1.4 Genome reference.............................. 5
1.5 General NGS analysis workflow ...................... 6
2 Related work ................................... 8
2.1 Commercial online analysis platforms ................... 8
2.2 Open source donline analysis platform................... 9
2.3 Pipeline execution tools........................... 12
2.4 Analysis report generation ......................... 14
3 Methods...................................... 17
3.1 RNA-Seq pipelines ............................. 17
3.2 DNA-Seq pipelines............................. 20
3.3 BioCloud website.............................. 21
3.3.1 Overview.............................. 21
3.3.2 Data integrity check and authentication............... 24
3.3.3 User account management ..................... 26
3.3.4 Data source management...................... 27
3.3.5 Experiment design ......................... 27
3.3.6 Genome reference ......................... 29
3.3.7 Analysis submission ........................ 30
3.3.8 Job queue management....................... 30
3.3.9 Report and result access control .................. 31
3.4 Report generation.............................. 33
3.4.1 Analysis result structure and information............... 33
3.4.2 BCReport: result processing framework............... 35
3.5 Implementation ............................... 36
3.5.1 Website............................... 37
3.5.2 Deployment............................. 38
3.5.3 Report................................ 39
4 Results....................................... 40
4.1 Datasets................................... 40
4.2 Account registration and user dashboard.................. 42
4.3 Data source discovery............................ 45
4.4 Experiment design ............................. 45
4.5 Analysis design............................... 50
4.6 Job queue monitoring............................ 52
4.7 Summary report............................... 54
4.7.1 Quality control ........................... 55
4.7.2 Genome alignment – STAR .................... 56
4.7.3 Cuffdiff............................... 58
4.7.4 Integration with external genome browsers ......... 60
4.8 Admin interface............................... 62
5 Discussions .................................... 64
5.1 Data source uploading ........................... 64
5.2 Supported analyses ............................. 65
5.3 Pipeline extension.............................. 65
5.4 Integration with other frameworks ..................... 67
6 Conclusions.................................... 69
Bibliography ..................................... 71

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