揭開生物體基因密碼的重要關鍵是全新基因體組序，而要得到基因體序列 的第一步是定序。目前最常見的定序平台是 Illumina，其優點是價錢低廉與錯 誤率低(1%)，缺點是定序長度較短(150bp)。另一種定序平台-PacBio 則有非常 長的定序長度(>10kb)，但錯誤率則較高(~15%)。目前市面上針對不同的定序平 台，開發了許多組序軟體。但目前都沒有定論哪一種組序方法較好，也沒有好 的方法評估全新基因體組序。在此我們測試不同組全新基因體序列的平台，並 且開發出評估全新基因體組序的方法。我們所使用的基因體是來自成功大學陳 逸民老師。他們在台灣找到可製造高量二十二碳六烯酸(DHA)的微藻，並將 其命名為 BL10。將 BL10 分別使用 Illumina 和 PacBio 定序平台定序，並在測 試各項參數後，成功組出其基因體序列。此外，我們除了評估組序後的長度外， 還更進一步探討組序後的序列內容正確性。我們將不同軟體組序後的基因體序 列兩兩比對，看彼此的相似程度。此外，還額外使用核糖核酸定序資料(RNA sequencing)比對回組序後的基因體序列，看比對上的好壞來評估組序出的基 因體序列優劣。使用上述這些數值成功評估出個各組序軟體的優劣與特性。這 套流程未來可使生物研究更便利，且幫助研究者更精確地選擇軟體。

De novo genome assembly reveals genetic codes and facilitates lots of biological studies. And sequencing is the first step to get genome sequence. Currently, there are various sequencing platforms. Illumina and PacBio nowadays are the most popular sequencing platform. To assemble these two kinds of read types, various assemblers have been published. But it remains uncertain which assembler or parameters are the best. And there is no good way to judge the performance of a de novo genome assembly. Here, we try to test several assemblers to assemble a new genome. And design a system to compare the performance of genome assemblies. We used Taiwan microalgae as de novo genome which is found by, Dr. Yi-Min Chen, and named BL10. We performed BL10 sequencing with Illumina and PacBio. After we finally assembling BL10 genome with difficulty, we successfully design a system to judge de novo genome assemblies. This system not only compares assembles quantity, for example, N50, but their quality. We use assembles comparing each other sequences to evaluate the quality. Besides, we use RNA transcripts aligning with assembles to decide which assembles is best. After evaluating different BL10 assemblies, hybrid assembler – MaSuRCA will assembly best BL10 genome. And this pipeline will facilitate biological research and help researchers to choose tool accurately.

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