Recently, Huawei Cloud and Peak Computer Computing (hereinafter referred to as “Fengkeâ€) released an FPGA-based gene acceleration cloud solution that uses GATK (The Genome Analysis Toolkit) standard analysis process to improve the performance of whole genome sequencing (WGS). It is 3 to 5 times higher than the traditional mode, and the sequencing accuracy can reach 99.95% or more. The TCO is greatly reduced while greatly reducing the sequencing time.
Gene sequencing data analysis accelerates the challenges
First, the gene sequencing analysis process BWT+GATK is currently widely adopted by the industry, but the traditional sequencing method using this process requires high computational power and storage resources, and takes a long time.
Secondly, smith-waterman, pair-hmm and other algorithms for high-computation requirements in gene sequencing have computational parallelism, discontinuous, irregular storage access, low-bit operation, etc. The CPU is very expensive and the performance is difficult to improve.
Three advantages of Huawei cloud FPGA gene acceleration solution
In order to better solve the genomic analysis standard process faced by the gene sequencing industry is not cost-effective, and the double challenge of accelerating implementation across different clouds and hardware (CPUs, FPGAs). Huawei Cloud and Fengke Computing have joined forces to jointly launch the GATK acceleration process in line with industry standards, and achieve end-to-end acceleration through software and hardware joint optimization of the gene sequencing data analysis process. Huawei Cloud FPGA Gene Acceleration Solution has the following advantages: First, Huawei Cloud provides the industry-leading FPGA-accelerated cloud service platform, adopts the industry-leading Xilinx 16nm Virtex UltraScale+ VU9P FPGA, and launches 32-core CPU224GB memory 1 VU9P FPGA and 64 core for genetic scenarios. CPU448GB memory 2 VU9P FPGA specification example, the perfect combination of GATK software processing flow and FPGA acceleration process, which will accelerate the acceleration efficiency by 3 to 5 times.
Secondly, Fengke uses the GATK standard analysis process, and the accuracy is completely consistent with the GATK standard process, with an accuracy of over 99.95%.
Third, without modifying the GATK standard process, you can access the intermediate data from the original sequencing data to the generation of the vcf file, which is convenient for scientific users to use.
1. Huawei cloud FPGA gene acceleration solution analysis
Huawei Cloud FPGA Gene Acceleration Solution integrates Peak's Accelerated IP to provide users with an easy-to-use, cost-effective FPGA-based genomic analysis process acceleration service. In this solution, Huawei Cloud is equipped with a 32-core CPU, a single VU9P FPGA. An example. The Huawei Cloud FPGA Gene Acceleration Solution uses GATK best practices to detect mutations in germline mutations and somatic mutations, and computes computationally intensive algorithms such as Smith-Waterman and PairHMM as acceleration targets. Each algorithm is optimized by the FPGA core and implements CPU-FPGA co-execution and resource allocation. As shown in Figure 2, the user passes the data of each process to the Huawei Yunfeng Acceleration Platform by analyzing the application, and the Kestrel runtime management tool in the platform manages CPU-FPGA collaborative execution and resource allocation. Utilizing multi-threading, I/O optimization and expansion using FPGA accelerators, the genomics analysis process of Huawei Cloud FPGA Gene Acceleration Services provides significant acceleration while ensuring accuracy.
Huawei Cloud FPGA Gene Acceleration Scheme Structure
In contrast to the GATK best use process, a typical gene sequencing data analysis process begins with the paired-end reads of the original FASTQ sequence, further obtaining a set of filtered variants, which are labeled for further analysis. . Figure 3 depicts the specific flow of the Huawei Cloud Gene Acceleration Service variability call pipeline. The middle panel indicates the normal workflow at the beginning. The top-level acceleration process and the GATK optimal use flow command are implemented in the Huawei cloud FPGA gene acceleration scheme. The way the workflow is.
Huawei Yunfeng Branch Gene Acceleration Process and GATK Best Use Process Comparison
Based on Huawei cloud FPGA acceleration service, using FPGA optimization to accelerate the GATK process, the genome analysis process can achieve 3 to 5 times faster speed and more than 99.95% accuracy. Huawei Cloud FPGA Gene Acceleration Solution The fastest genomic sequence analysis standard process can complete 5 whole genomes or 24 whole exome analysis in one day.
Performance comparison for GATK 3.8 WGS from Alignment to Variant Calling using Hoplotypecaller
Cloud based comparisonTotal(Hrs.)Speedup
WGS(30X)Falcon on Huawei7.464.84x
Original 36.11x
Note: The test data is a 30X WGS sample, and the number of bases is 103G Huawei Cloud Gene Acceleration Service “0†meta-experience
In order to enable more users to experience Huawei cloud FPGA acceleration cloud server, Huawei Cloud United Fungke (Falcon) launched the "gene acceleration service 0 yuan experience package" for the gene acceleration scenario. The package specification is 32 core CPU224GB memory 500GB data disk 5M. bandwidth.
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