- 學位論文
HiCNextflow:一個靈活且具再現性的Hi-C分析平台
HiCNextflow: a flexible and reproducible Hi-C workflow
摘要
我們建立一個以Nextflow為框架的Hi-C分析平台。 Hi-C分析是一個複雜的流程，包括多個步驟：對齊 (mapping)、過濾 (filtering) 和環形(looping) 。首先我們選用現有流程中所使用的對齊工具，評估其對齊的效率，並觀察對後續環形個數的影響，透過視覺化來分析其影響效益，總結地為Hi-C分析平台找到最佳的對齊工具。此外流程中各步驟均依據上一步的輸出結果來當作輸入值，因此開發流程時，容錯是關鍵的問題， 當發生錯誤時，重新執行應該僅從失敗的地方開始重跑，而不需要從頭開始執行。 我們根據Nextflow設計新穎的Hi-C分析平台，從而簡化複雜的平行運算和互動式工作流程，而它將使我們的流程更快且更有效率。
並列摘要
We are planning to implement a Hi-C analysis pipeline based on the Nextflow framework. Hi-C analysis is a complex pipeline that includes multiple steps: mapping, filtering, loop calling, and parallelization. Each step is based on the outputs of the previous step. Fault tolerance is a critical issue in developing the pipeline. When a fault happens, the rerunning pipeline should only start from the fail step instead of rerunning from the beginning. We will choose some mapping tools used by existing pipelines. Then we execute them according to our planned workflow. We will find the optimal mapping tool for our pipeline from these methods based on the number of called loops and visualized graphs. We designed a novel Hi-C analysis pipeline based on Nextflow, which simplifies the implementation and the deployment of complex parallel and reactive workflows. It makes our pipeline more quickly and more efficiently.