Illumina MiSeq and iSeq platforms yield comparable results for viral genomic sequencing

Illumina systems are the predominant short-read NGS technology, with the MiSeq considered standard platform for mid-range throughput. In comparison, the iSeq platform, with its lower instrumentation cost, is well-suited for labs new to NGS or in locations where on-site maintenance would be difficult to arrange. In the current study, differences in quality metrics and assembly were compared through sequencing of SARS-CoV-2, norovirus, and Polio genomes on the two platforms. Quality metrics for reads tended to differ across MiSeq and iSeq. For SARS-CoV-2, MiSeq paired reads had lower percentage > Q30 than iSeq paired reads even after adapter trimming. By contrast, untrimmed norovirus MiSeq paired reads were statistically equivalent with iSeq paired reads. Similarly, poliovirus MiSeq paired reads were statistically equivalent with iSeq paired reads, but only after adapter trimming. MiSeq and iSeq insert lengths were also statistically distinct, both before and after trimming. Despite differences in MiSeq and iSeq quality metrics, analysis results, such as SNPs and genomic assemblies, tended to be equivalent. SARS-CoV-2, norovirus, and poliovirus exhibited MiSeq to iSeq SNPs concordance. Following adapter removal, the two platforms generated equivalent de novo genome assembly metrics, with statistically equivalent mean N50 values observed for MiSeq and iSeq SARS-CoV-2, norovirus, and poliovirus datasets. iSeq provides a more cost-effective choice for low-throughput sequencing or labs not specializing in NGS. By contrast, MiSeq is more cost-effective for labs implementing high-throughput NGS or requiring more versatility in sequencing a wide range of pathogens.