建構全面性細菌基因體全新組裝之線上系統

現今隨著次世代定序技術之成本顯著下降，建構未知細菌物種的完整基因體或是從環境樣本中提取大量微生物資訊對於研究者而言更為容易，在細菌的定序資料不斷增加累積之下，細菌基因體的相關研究重要性不斷上升，更逐漸成為生物資訊的熱門研究主題。完整基因體的組裝可以有助於了解生物之相關功能和訊息傳輸方式，而如今也有相當多的生物資訊工具和演算法被開發來研究原核生物基因序列，不過如何有效的組合各第三方軟體來創建有效的分析流程是為一大挑戰，尤其複雜的參數設定和以指令列為基礎的軟體操作更成為了研究者分析的阻礙。為了有效解決上列問題，我們以創建對使用者友善的線上分析系統為目標，旨在提供有效而易於操作的細菌全新基因體組裝和宏基因體學資料分析流程，並以Illumina公司平台產出之次世代定序資料作為輸入，在系統中直接提供包括序列品質評估、基因體組裝、基因預測以及基因功能性分析等功能。整體而言，此平台將可大幅節省研究者進行細菌基因體全新組裝或是分析環境樣本的時間與精力，有助於使用者專注深入瞭解目標細菌之致病性或是微生物之生態組成。

關鍵字

細菌；全新組裝；宏基因體學；使用者友善；線上系統

並列摘要

Nowadays, the substantial reduction of experimental cost in the next-generation sequencing techniques makes it feasible to assemble a de novo bacterial genome of unknown species and acquire plenty of genetic information from environmental samples. With the explosive accumulation of bacterial sequencing data, the research focusing on bacterial genome has become more and more important and popular. The development of the whole genome can help to elucidate biological functions and signaling pathways. Many bioinformatics tools and algorithms have been developed to study prokaryotic genome; however, how to efficiently construct pipelines to integrate all the data poses a major challenge. Complex parameters settings and the command line-based packages cause a great entry barrier for researchers. To address these issues, this study aims to develop an online analytical system with a user-friendly interface to support both de novo assembling and metagenomic analysis pipelines. Multiple analytical steps, including reads cleaning, genome assembly, gene prediction, and functional annotation can be directly performed on the system. In conclusion, this analytical system can greatly reduce the time and efforts for assembling a de novo bacterial genome and analyzing metagenomic samples, which can improve the understanding of the etiology in targeting bacterial species and the ecology of microorganisms.

並列關鍵字

bacteria ； de novo assembly ； metagenomics ； user-friendly ； online system

參考文獻

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國際替代計量

建構全面性細菌基因體全新組裝之線上系統

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