Shulou(Shulou.com)06/02 Report--

Introduction: in 2015, Aliyun and BGI set a goal: to complete the sequencing of their entire genome in 24 hours by 2020. This was an almost impossible challenge at the time. On the 17th day of 2020, we achieved this goal! And it takes only 15 minutes to sequence an individual's whole genome, less than a meal.

Large-scale flexible scheduling computing in the cloud

Figure 1-schematic diagram of WGS analysis process

The challenges faced by genetic computing are different from conventional computing. Big data Shengxin analysis platform needs to have PB-level data processing capabilities: storage and compression, cleaning and management, low-cost preservation, fast and secure cloud distribution and sharing, security and privacy protection of genetic data, large-scale data mining, on-demand scheduling and flexible expansion, etc.

This solution is formed by the deep integration of Huada DNBSEQ self-sequencer, BGI Online hybrid cloud architecture, Ali Cloud Container Service ACK/AGS Gene Service and Xylar Gene GPU acceleration algorithm. Among them, the overall technical architecture of BGI and Aliyun is cloud native container hybrid cloud, realizing the integration of resources on the cloud and under the cloud, and unified management across regional clusters. With the automatic scaling feature of the cloud, large-scale flexible scheduling computing is realized.

In use, users of this scheme do not need to pay attention to the details of computing resources, processing logic and data cache in the process of genetic data processing, but only need to upload the offline data (FASTQ file) to OSS and authorize Bucket to AGS service, so that the whole data analysis process can be completed efficiently and quickly, and the resulting data can be uploaded to the desired storage space.

This end-to-end solution seamlessly connects the sequencing platform and the gene cloud platform, fully supports a variety of sequencing platforms, including the DNBSEQ series sequencers, and can customize the analysis process on demand with high delivery flexibility.

Faster, more accurate, and lower cost

Compared with similar products, it has great advantages in computing speed, accuracy, cost, ease of use and integration with upstream sequencers. In 2020, the new WGS delivery program will help genetic research and clinical testing to a new level.

After the actual test, the whole scheme completed the secondary analysis and processing of 8 groups of 30X WGS samples in 15 minutes. On the premise of ensuring the accuracy, the assembly, sequencing, weight removal and mutation detection of 720 billion bases are realized in 15 minutes, and the whole process of gene detection is accelerated by 120 times. And after comparing the NA12878 test data set with the gold standard VCF, the accuracy of the secondary analysis is higher than or equal to the data output of BWA-0.7.17/GATK 4.1.3, and the SNP accuracy reaches 99.80%!

Figure 2-acceleration effect of measured 30x WGS N12878 data

Figure 3-30x WGS Software acceleration consistency

At the same time, Aliyun ACK/AGS provides cloud PaaS acceleration capability to assist BGI to complete the near real-time delivery of mass offline data analysis of independent sequencer in a hybrid cloud, which can effectively reduce the cost of analysis and calculation and shorten the delivery cycle of this process.

Speed up the process of decoding life

Previously, offline WGS analysis of a single sample usually takes 70 hours; at the end of 2016, BGI Online (international version) achieved 17 hours to complete 100 WGS analysis; at the end of 2017, the time was reduced to 120 minutes; now, together with Aliyun, it has set a new record of 15 minutes to complete a WGS, and BGI Online has once again refreshed the speed limit of genome-wide analysis.

With the launch of the accurate medical population cohort project, the independent and controllable gene sequencing and analysis platform in China is becoming more and more important. BGI Online will continue to improve the functions of the platform in the future, provide users with a complete, comprehensive and friendly functional experience, and make the research in the field of bioinformatics more simple and efficient.

Decode the unknown, measure life. Every small step in science and technology will become a big step forward for mankind. BGI and BGI Online will continue to work together with partners to contribute to the genetic cause.

Note: human whole genome sequencing (Whole Genome Sequencing, referred to as WGS) is a method that uses high-throughput sequencing technology to sequence the whole genome of different human individuals or groups and analyze bioinformatics. In-depth analysis of cancer and genetic diseases often requires WGS sequencing and analysis of a large number of samples, and the mining of WGS data can also find a lot of valuable genetic diversity information. There are 3 billion bases in a human genome, and the amount of data of a 30x WGS is about 100G.

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