Benchmarking Next-Generation Sequencing Platforms: A Comprehensive Comparison Of Single-Cell RNA-Seq from Ultima UG 100 vs. Illumina NovaSeq X Plus

Xiong, R.; Patel, J.; Sztanka-Toth, T.; Senel, E.; Calara-Nielsen, K.; Rajpurohit, Y.; Altenburg, T.; Greshock, J.; Smirnov, D.; Javidi, A.

doi:10.64898/2026.01.16.699571

bioRxiv · 10.64898/2026.01.16.699571

Benchmarking Next-Generation Sequencing Platforms: A Comprehensive Comparison Of Single-Cell RNA-Seq from Ultima UG 100 vs. Illumina NovaSeq X Plus

Xiong, R.·Patel, J.·Sztanka-Toth, T.·Senel, E.·Calara-Nielsen, K.·Rajpurohit, Y.·Altenburg, T.·Greshock, J.·Smirnov, D.·Javidi, A.

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Abstract

Single-cell RNA sequencing (scRNA-seq) has become an essential technology for dissecting cellular heterogeneity in complex biological systems, with Illumina platforms serving as the dominant NGS provider1-3. The recent emergence of the Ultima Genomics UG 100 platform offers a high-throughput and potentially more cost-effective alternative, warranting a rigorous comparative analysis. Here, we conducted a comprehensive head-to-head comparison of the Ultima Genomics UG 100 and Illumina NovaSeq X Plus platforms, generating deep-coverage scRNA-seq data from human PBMCs and stimulated T-cell samples. Our multi-level analysis revealed highly concordant performance in both cell type identification and gene expression. We found that both platforms robustly captured all major immune lineages and demonstrated good transcriptional agreement. Minor observed discrepancies were primarily correlated with low UMI counts, suggesting stochastic biological effects rather than technical variance. Overall, our study establishes that the Ultima UG 100 delivers performance highly comparable to the Illumina NovaSeq X Plus for single-cell transcriptomics.

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Xiong, R., Patel, J., Sztanka-Toth, T., Senel, E., Calara-Nielsen, K., Rajpurohit, Y., Altenburg, T., Greshock, J., Smirnov, D., Javidi, A.. 2026-01-20. Benchmarking Next-Generation Sequencing Platforms: A Comprehensive Comparison Of Single-Cell RNA-Seq from Ultima UG 100 vs. Illumina NovaSeq X Plus. https://doi.org/10.64898/2026.01.16.699571

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