QIAGEN Bioinformatics*

QIAGEN Bioinformatics* solutions deliver faster time to insight by combining powerful analytics that are able to interpret complex biological processes.

Analyze Whole Human Genomes for as Little as USD 22

The QIAGEN Biomedical Genomics Server* solution is able to minimize the total cost of ownership (TCO) over a four-year period for the largest NGS instrument on today's market. Calculations of the total ownership costs show that with given specifications, the cost can be as low as USD 22 per whole human genome analyzed.1 2 With very high throughput enabled by a HiSeq X Ten*, the savings can be sizable.

Performance Results

An Illumina HiSeq X Ten* system is able to sequence a total of 18,000 whole genome sequences per year—averaging the rate of analysis to 30 minutes per one whole human genome sequence. By optimizing and fine-tuning the speed of the QIAGEN Biomedical Genomics Server* solution, we demonstrated that the solution is able to analyze the NGS data at the pace they are produced by the instrument running at maximum throughput— with less computing nodes than recommended by others3. The testing scenario revealed that QIAGEN Biomedical Genomics Server requires a compute cluster of only 32 nodes, as contrasted (in contrast) to the 85 nodes recommended by Illumina (variant calling based on BWA+GATK Best Practices pipeline in the HiSeq X system lab setup and Site Prep Guide (Document 15050093 v03, January 2016). The comparison benchmark testing was carried out by installing the QIAGEN Biomedical Genomics Server solution on a compute cluster of 32 nodes.1 2 each equipped with a 28-core E5-2697 v3 @ 2.60GHz, 128 GB RAM on a shared Lustre file system. We used the standard CLC variant calling workflow that comes with the Biomedical Genomics Server solution. Furthermore the benchmarks show that the same specified system is capable of analyzing up to 1440 whole human exomes per 24 hours.

Total Cost of Ownership

Reducing the hardware requirements from 85 nodes to just 32 nodes results in a dramatic impact on the total cost of ownership on the solution over a four-year period, which includes everything from software licenses and hardware, to power, cooling, networking, and floor space. Calculations of the total ownership costs show that the cost can be brought down as low as USD 22 per whole human genome analysis. Given the 18,000 whole human genome throughput enabled by a HiSeq X Ten, the savings can be as high as USD 1.3 million over four years. Additional benchmarks also show that the reference architecture is capable of analyzing up to 1,440 whole exome sequences per 24 hours.

Size and scale your infrastructure according to your workloads with the QIAGEN* reference architecture ›

產品與效能資訊

1

根據由 QIAGEN Bioinformatics 和 Intel 所進行的內部效能測試與總持有成本分析。效能測試於 16 節點的高效能運算 (HPC) 叢集上進行。每個節點皆使用 2 個 Intel® Xeon® 處理器 E5-2697 v3(2.6 GHz,14 核心)、128 GB 記憶體,以及 500 GB 的儲存磁碟機。所有節點共用以 Intel® Enterprise Edition for Lustre* 軟體(Intel® EE for Lustre* 軟體)為基礎的 165 TB 儲存系統、256 TB 的 1000 RPM 磁碟儲存空間,以及 4 個 800 GB Intel® 固態硬碟資料中心 S3700 系列。互連結構的每個節點搭載 2 個 Intel® True Scale Architecture 單連接埠 HCA(2 個 QLE7340,QDR-80),以及 36 連接埠的 Intel® True Scale Switch Firmware 12300 (40 Gbps)。TCO 分析使用內部 Intel® 工具與截至 2015 年 10 月 9 日公開可用的產品定價與可用度。測試叢集的 TCO 估計採用 4 年週期,並與 Illumina HiSeq X System Lab Setup and Site Prep Guide(Illumina HiSeq X 系統研究室設置與場所準備指南,文章編號 15050093 v05,2017 年 1 月)中所述的 85 節點叢集的預估 TCO 相比較。為了量化 TCO 的比較結果,特別選擇了符合 Illumina 指南中所定義之通用規格的產品。兩種系統的支援成本皆估計為 TCO 的百分之 60。效能與 TCO 結果應僅做為通用指南,以評估未來購買系統的成本/優勢或可行性。實際效能結果與經濟效益將會有所出入,並可能包括與使用和部署解決方案相關的額外未計入成本,這些因素可能無法計算。效能測試中使用的軟體與工作負載可能僅針對 Intel® 微處理器進行最佳化。包括 SYSmark* 與 MobileMark* 在內的效能測試是使用特定電腦系統、零組件、軟體、作業與功能進行量測。這些因素若有任何異動,均可能導致測得結果產生變化。建議您參考其他資訊與效能測試數據,協助您充分評估欲購買產品的性能,包括該產品在搭配其他產品運作時的效能。如需詳細資訊,請參閱 http://www.intel.com.tw/performance

2

效能測試所使用的 WGS 資料集為 NA12878D,由 Illumina 的 TruSeq Nano* 套件使用 350bp 輸入所產生,並在單一線道的 Illumina HiSeq X* 上定序,具有大於 87% 的基礎,且品質大於 Q30。平均覆蓋率:35.57%,讀取長度:2 x 151,120 Gb。您可以在 https://dnanexus-rnd.s3.amazonaws.com/NA12878-xten.html 存取此資料集。

3

效能標竿結果是在實施最近的軟體修補程式與韌體更新以解決「Spectre」和「Meltdown」安全漏洞之前取得的資料。實施這些更新可能會讓這些結果變得不適用於您的裝置或系統。

效能測試中使用的軟體與工作負載可能僅針對 Intel® 微處理器進行最佳化。包括 SYSmark* 與 MobileMark* 在內的效能測試是使用特定電腦系統、零組件、軟體、作業與功能進行量測。這些因素若有任何異動,均可能導致測得結果產生變化。建議您參考其他資訊與效能測試數據,協助您充分評估欲購買產品的性能,包括該產品在搭配其他產品運作時的效能。如需完整的資訊,請參閱 http://www.intel.com.tw/benchmarks