Duplication Rates
The MGISEQ-2000 exhibited a lower duplication rate compared to the Illumina HiSeq 2500 when analyzing individual fastq files. The overall duplication rate for the Illumina platform was higher (12.26%) due to the merging of fastq files from two different flow cells, while the duplication rate for both platforms did not exceed 5-6% in individual files.
Data Generation and Coverage
Both platforms generated comparable amounts of data, with MGISEQ-2000 producing 101.37 Gb and HiSeq 2500 producing 94.37 Gb. The average coverage was also similar, with MGISEQ-2000 at 32.75X and HiSeq 2500 at 30.48X, indicating that both platforms provide similar sequencing quality.
Error Rates and Variant Detection
The study found that while the MGISEQ-2000 had slightly inferior performance in terms of random sequencing errors and indel detection accuracy, the differences were small and generally insignificant for most research tasks. The detection rates of genomic variants were similar between the two platforms, suggesting that they can be used interchangeably for many applications,.
Library Preparation Methods
Different methods of DNA fragmentation were used for library preparation, with MGISEQ-2000 utilizing ultrasound fragmentation and Illumina HiSeq 2500 using enzymatic fragmentation. This difference in preparation methods is important for interpreting the results.
Overall, while both platforms demonstrated comparable performance in many aspects, the MGISEQ-2000 can be considered a viable alternative to the Illumina HiSeq 2500 for whole-genome sequencing tasks.
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