Abstract
Background MGISEQ-2000 developed by MGI Tech Co. Ltd. (a subsidiary of the BGI Group) is a new competitor of such next-generation sequencing platforms as NovaSeq and HiSeq (Illumina). Its sequencing principle relies on the DNB and cPAS technologies also used in the previous version of the BGISEQ-500 device, but the reagents for MGISEQ-2000 are refined and the platform utilizes updated software. The cPAS technology has evolved from cPAL previously created by Complete Genomics.
Findings This article compares the results of the whole-genome sequencing of a DNA sample from a Russian female donor performed on MGISEQ-2000 and Illumina HiSeq 2500 (both PE150). Two platforms were compared in terms of sequencing quality, number of errors and performance. Additionally, we did variant calling using four different software packages: Samtools mpileaup, Strelka2, Sentieon, and GATK.
Conclusions The accuracy of single nucleotide polymorphism (SNP) detection was similar between the data generated by MGISEQ-2000 and HiSeq 2500, which was used as a reference:
For Samtools mpileaup software package: TPR (Sensitivity) 99.30%, FPR = 0,000498%;
For Strelka2 software package: TPR (Sensitivity) 99,51%, FPR = 0,000254%;
For Sentieon software package: TPR (Sensitivity) 99,57%, FPR = 0,000285%.
For GATK software package: TPR (Sensitivity) 98,70%, FPR = 0,000240%.
At the same time, a separate indel analysis of the overall error rate revealed similar FPR values and lower sensitivity:
For Samtools mpileup: TPR (Sensitivity) 93,62%, FPR = 0,000698%;
For Strelka2: TPR (Sensitivity) 98,84%, FPR = 0,000127%;
For Sentieon: TPR (Sensitivity) 98,68%, FPR = 0,000285%.
For GATK: TPR (Sensitivity) - 98,70%, FPR = 0,000240%.
The method of statistical analysis we use does not allow us to conclusively establish which of the two instruments is the most accurate. However, it can be said with confidence that the data generated by the analyzed sequencing systems are characterized by the comparable magnitude of error and that MGISEQ-2000 can be used for a wide range of research tasks on a par with HiSeq 2500.
