Revolutionizing Next-Generation Sequencing 2023, Ghent, Belgium
RNA-seq benchmarking study on existing and new state-of-the-art sequencing technologies at the VIB Nucleomics Core
Kizi Coeck, Lim De Swert, Rekin’s Janky, Kobe Lavaerts, Ruth Maes, Stéphane Plaisance, Emily Sheridan, Thomas Standaert, Jolien Vandewinkel, Stefaan Derveaux
VIB Nucleomics Core – Leuven, Belgium
With many competing DNA sequencing platforms now available, NGS users have a need for comparative studies that highlight the relative strengths of different platforms. Here, we report the results of same-sample sequencing runs on the Element, MGI, and Illumina platforms. ERCC-spiked UHRR and HBRR were mixed at 4 different ratios. Illumina Stranded Total RNA Library preparation was applied to 4 replicates of each mix. Libraries were equimolarly pooled and aliquots of the very same pool were paired-end 150bp sequenced on NovaSeq6000 SP, NextSeq2000 P3, AVITI, and G400 FCL. Conversion steps were introduced following instructions by the providers to make the pool compatible with AVITI and G400 sequencing. Differences in run consistency, percent duplication, and accuracy are presented in detail. The highest Quality Scores were obtained on the AVITI, with 98,5% of bases >Q30 (corresponding to 95% > Q40), followed by the G400. On the other evaluated platforms, the fraction of bases >Q30 was 92%, 95% and 92,5% f respectively for the NovaSeq6000, G400 and NextSeq2000.