Comparison of Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400 for Ancient DNA Whole-Genome Sequencing
Abstract
1. Introduction
2. Materials and Methods
3. Results
3.1. Comparing Base NGS Data Parameters
3.2. Population Genetic Analyses
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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| Sample ID | Burial | Date 1 | Sex 2 | Age, Years | Radiocarbon Dating | ||
|---|---|---|---|---|---|---|---|
| Laboratory Number | Radiocarbon Determination | Calibrated Data INCAL20, 95.4% | |||||
| Fan25 | Eastern necropolis, 256/2013 1 | Hellenistic period, 2 c. BCE | M 3 | 10 | GV-6662 | 2093 ± 23 BP | 172–45 calBCE |
| Fan46 | Southern necropolis, 288/2012 1 | Classical period, first quarter 4 c. BCE | F | ≈50 | GV-5850 | 2500 ± 36 BP | 784–483 calBCE |
| Fan52 | Eastern necropolis, 194/2013 | Roman period | M | 40–49 | GV-6663 | 2276 ± 24 BP | 400–209 calBCE |
| Fan64 | Eastern necropolis, 226/2014 | Roman period | M 3 | 10–11 | GV-6025 | 2069 ± 36 BP | 176 calBCE–24 calCE |
| FanKht01 | Upper Town, Object 749/2016 | 2 c. CE | M | ≈50 | GV-6026 | 2038 ± 35 BP | 154 calBCE–65 calCE |
| FanKht03 | Lower Town, Object 10/2016, spit 15 | Khazar time, 7–9 c. CE | – | 6–7 | GV-6028 | 1288 ± 35 BP | 658–821 calCE |
| Platform | Reagent Kit | Flow Cell Type | Ampification Type | Sequencing Chemistry Type | Read Number (M) Yield | |
|---|---|---|---|---|---|---|
| Expected | Observed | |||||
| Illumina NovaSeq 6000 | SP Reagent Kit v1.5 (100 cycles) | Patterned | Bridge | 2-colour | 800 | 940 ± 70 1 |
| S4 Reagent Kit v1.5 (35 cycles) | 10,000 | 12,659 ± 743 2 | ||||
| GeneMind SURFSeq 5000 | Sequencing Kit V2.0 (FCP 300 cycles) | Patterned | Bridge | 4-colour | 3600 | 4225 |
| Salus Evo | PRH-PE-150-1500M | Random | Bridge | 4-colour | 1500 | 1876 |
| MGI DNBSEQ-G400 | DNBSEQ-G400RC FCL SE100 | Patterned | Rolling circle | 4-colour | 1500 | 2190 |
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Manakhov, A.D.; Rozhdestvenskikh, E.V.; Aituganova, E.D.; Voroshilov, A.N.; Svirkina, N.G.; Kunizheva, S.S.; Andreeva, T.V.; Ostapenko, S.N.; Kuznetsov, V.D.; Rogaev, E.I. Comparison of Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400 for Ancient DNA Whole-Genome Sequencing. Genes 2026, 17, 853. https://doi.org/10.3390/genes17080853
Manakhov AD, Rozhdestvenskikh EV, Aituganova ED, Voroshilov AN, Svirkina NG, Kunizheva SS, Andreeva TV, Ostapenko SN, Kuznetsov VD, Rogaev EI. Comparison of Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400 for Ancient DNA Whole-Genome Sequencing. Genes. 2026; 17(8):853. https://doi.org/10.3390/genes17080853
Chicago/Turabian StyleManakhov, Andrey D., Elizaveta V. Rozhdestvenskikh, Eleonora D. Aituganova, Aleksej N. Voroshilov, Natalia G. Svirkina, Svetlana S. Kunizheva, Tatiana V. Andreeva, Sergey N. Ostapenko, Vladimir D. Kuznetsov, and Evgeny I. Rogaev. 2026. "Comparison of Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400 for Ancient DNA Whole-Genome Sequencing" Genes 17, no. 8: 853. https://doi.org/10.3390/genes17080853
APA StyleManakhov, A. D., Rozhdestvenskikh, E. V., Aituganova, E. D., Voroshilov, A. N., Svirkina, N. G., Kunizheva, S. S., Andreeva, T. V., Ostapenko, S. N., Kuznetsov, V. D., & Rogaev, E. I. (2026). Comparison of Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400 for Ancient DNA Whole-Genome Sequencing. Genes, 17(8), 853. https://doi.org/10.3390/genes17080853

