Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing
Abstract DNA sequencing technology has significantly advanced over the past five decades, particularly with the introduction of next-generation sequencing (NGS) platforms like Illumina’s NovaSeq. In October 2023, Sikun introduced the Sikun 2000, a desktop NGS platform designed for rapid, cost-effect...
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Nature Portfolio
2025-05-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-04170-6 |
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| author | Keya Cai Sibin Li Meng Pan Hui Lu Liang Wang Shengquan Fang Lingzhi Gou Jiang Tang Yan Kong Li Zhao Yongyong Ren |
| author_facet | Keya Cai Sibin Li Meng Pan Hui Lu Liang Wang Shengquan Fang Lingzhi Gou Jiang Tang Yan Kong Li Zhao Yongyong Ren |
| author_sort | Keya Cai |
| collection | DOAJ |
| description | Abstract DNA sequencing technology has significantly advanced over the past five decades, particularly with the introduction of next-generation sequencing (NGS) platforms like Illumina’s NovaSeq. In October 2023, Sikun introduced the Sikun 2000, a desktop NGS platform designed for rapid, cost-effective sequencing with up to 200 Gb of data per run. This study is the first to evaluate the performance of the Sikun 2000 in whole genome sequencing (WGS) and compares it with the Illumina NovaSeq 6000 and NovaSeq X platforms using five well-characterized human Genomes in a Bottle dataset. Results show that the Sikun 2000 performs competitively in variant detection, particularly excelling in single nucleotide variant accuracy. It also demonstrated a higher sequencing depth and lower proportion of low-quality reads than the NovaSeq platforms. However, its performance in insertion-deletion (Indel) detection was slightly lower than that of NovaSeq platforms. Overall, the Sikun 2000 is a qualified sequencing platform for WGS, and further evaluation in clinical and research applications is required as data continues to accumulate. |
| format | Article |
| id | doaj-art-8d4e952774a748d2a9afd59cf63cec7e |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-8d4e952774a748d2a9afd59cf63cec7e2025-08-20T04:02:45ZengNature PortfolioScientific Reports2045-23222025-05-011511810.1038/s41598-025-04170-6Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencingKeya Cai0Sibin Li1Meng Pan2Hui Lu3Liang Wang4Shengquan Fang5Lingzhi Gou6Jiang Tang7Yan Kong8Li Zhao9Yongyong Ren10Sikun Life Science Company LimitedSikun Life Science Company LimitedSJTU-Yale Joint Center for Biostatistics and Data Science, Technical Center for Digital Medicine, National Center for Translational Medicine, Shanghai Jiao Tong UniversitySJTU-Yale Joint Center for Biostatistics and Data Science, Technical Center for Digital Medicine, National Center for Translational Medicine, Shanghai Jiao Tong UniversitySikun Life Science Company LimitedDepartment of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese MedicineSikun Life Science Company LimitedSikun Life Science Company LimitedSJTU-Yale Joint Center for Biostatistics and Data Science, Technical Center for Digital Medicine, National Center for Translational Medicine, Shanghai Jiao Tong UniversitySikun Life Science Company LimitedSJTU-Yale Joint Center for Biostatistics and Data Science, Technical Center for Digital Medicine, National Center for Translational Medicine, Shanghai Jiao Tong UniversityAbstract DNA sequencing technology has significantly advanced over the past five decades, particularly with the introduction of next-generation sequencing (NGS) platforms like Illumina’s NovaSeq. In October 2023, Sikun introduced the Sikun 2000, a desktop NGS platform designed for rapid, cost-effective sequencing with up to 200 Gb of data per run. This study is the first to evaluate the performance of the Sikun 2000 in whole genome sequencing (WGS) and compares it with the Illumina NovaSeq 6000 and NovaSeq X platforms using five well-characterized human Genomes in a Bottle dataset. Results show that the Sikun 2000 performs competitively in variant detection, particularly excelling in single nucleotide variant accuracy. It also demonstrated a higher sequencing depth and lower proportion of low-quality reads than the NovaSeq platforms. However, its performance in insertion-deletion (Indel) detection was slightly lower than that of NovaSeq platforms. Overall, the Sikun 2000 is a qualified sequencing platform for WGS, and further evaluation in clinical and research applications is required as data continues to accumulate.https://doi.org/10.1038/s41598-025-04170-6Whole genome sequencingSikun 2000Variation detection |
| spellingShingle | Keya Cai Sibin Li Meng Pan Hui Lu Liang Wang Shengquan Fang Lingzhi Gou Jiang Tang Yan Kong Li Zhao Yongyong Ren Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing Scientific Reports Whole genome sequencing Sikun 2000 Variation detection |
| title | Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing |
| title_full | Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing |
| title_fullStr | Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing |
| title_full_unstemmed | Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing |
| title_short | Comparative assessment of the Sikun 2000 sequencing platform for whole genome sequencing |
| title_sort | comparative assessment of the sikun 2000 sequencing platform for whole genome sequencing |
| topic | Whole genome sequencing Sikun 2000 Variation detection |
| url | https://doi.org/10.1038/s41598-025-04170-6 |
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