Results of testing the Nanophor SPS whole-genome sequencer

Highlights More than 95% of nucleotide bases generated by the Nanophor SPS platform have a Phred quality score (Q) > 30, corresponding to a base-call accuracy of >99.9%. Successful de novo assembly of the complete viral genome was achieved, reconstructed as a single contig of 160,711 bp with a mean coverage of 300x. A significantly lower cost per sequencing run and operational expenses were confirmed compared to the MiSeq platform. Relevance. Relevance is driven by the need to develop domestic, cost-effective sequencing platforms for the genomes of dangerous pathogens, enabling rapid genomic surveillance of biological threats by the Nuclear, Biological, and Chemical (NBC) defense troops. Purpose of the study is to conduct a comprehensive performance assessment of the domestic whole-genome sequencing   system "Nanophor SPS" (Sintol, Russia) in comparison with the foreign counterpart MiSeq (Illumina, USA). Materials and Methods. A large DNA virus, Vaccinia virus strain B-51, was used as the test object. The methodology included DNA extraction, library preparation, whole-genome sequencing on both platforms, and subsequent comparative bioinformatic analysis. Results. The experimental validation demonstrated that the Nanophor SPS platform exhibits high performance and reliability, providing data quality comparable to the foreign sequencer (MiSeq, Illumina, USA). Conclusion. The domestic Nanophor SPS platform has confirmed its status as a productive, reliable, and cost-effective system that delivers data quality and analytical capabilities comparable to foreign analogues. It is recommended for implementation into the laboratory practice of the NBC defense troops. Practical significance of the work. The study provides the customer (NBC defense troops) with comprehensive, verified data to support an informed selection and procurement of a domestic sequencing platform, thereby contributing to reduced technological dependence. A ready-to-use protocol and reference benchmarks have been established for employing the Nanophor SPS system in the specific tasks of military laboratory diagnostics and biomonitoring.

1. Petrov AA, Kazantsev AV, Kovalchuk EA, Pavlyukov MYu, Sapkulov AV, Kutaev DA, Borisevich SV. Modern Hardware and Software Solutions for Whole-Genome Sequencing, Prospects of Their Implementation in the Practice of Nuclear, Chemical and Biological Protection Troops of the Armed Forces of the Russian Federation. Journal of NBC Protection Corps. 2024;8(2):164-175. (In Russ.). https://doi.org/10.35825/2587-5728-2024-8-2-164-175

2. Goodwin S, McPherson JD, McCombie WR. Coming of age: Ten years of next-generation sequencing technologies. Nature Reviews Genetics. 2016;17(6):333–351. https://doi.org/10.1038/nrg.2016.49

3. Alekseev YaI, Petrov AI, Chubinsky-Nadezhdin IV, Reznik VS, Nikanorov VV, Pushkin AA, et al. The first domestic device for massive parallel DNA sequencing Nanophore SPS. Biomics. 2025;17(2):121-32 (In Russ.). https://doi.org/10.31301/2221-6197.bmcs.2025-9

4. Manoilov VV, Borodinov AG, Saraev AS, Petrov AI, Zarutsky IV, Kurochkin VE. Image processing algorithms in the DNA sequencer Nanophor SPS. Technical Physics. 2022;92(7):985–92 (In Russ.). https://doi.org/10.21883/JTF.2022.07.52655.318-21

5. Mardis ER. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics. 2008;9:387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359

6. Ravi RK, Walton K, Khosroheidari M. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis. Methods Mol Biol. 2018;1706:223–32. https://doi.org/10.1007/978-1-4939-7471-9_12

7. Gregory SG. Contig Assembly. Encyclopedia of Life Sciences. Chichester: John Wiley & Sons, Ltd; 2005. https://doi.org/10.1038/npg.els.0005365

8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77. https://doi.org/10.1089/cmb.2012.0021

9. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010

10. Manoilov VV, Borodinov AG, Zarutsky IV, Petrov AI, Saraev AS, Kurochkin VE. Algorithms for the primary analysis of local fluorescence objects in the Nanophor SPS DNA sequencer. Informatics and automation. 2024; 23(4):989–1021 (In Russ.). https://doi.org/10.15622/ia.23.4.3

11. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. 2018;36(4):338–345. https://doi.org/10.1038/nbt.4060