Systematic performance evaluation and application validation of an end-to-end NGS workstation

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Systematic performance evaluation and application validation of an end-to-end NGS workstation

Scientific Reports , Article number:  (2026) Cite this article

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Abstract

Next-generation sequencing (NGS) library preparation is a core component of precision genomics, but it is commonly constrained by inefficiency, variability, and low throughput of manual protocols. To address these limitations, we developed and systematically evaluated a fully automated NGS workstations and further validated its performance across representative application scenarios. The automated system reduced total processing time from 8 to 10 to 4–6 h. At the same time, it maintained similar performance in pre-library metric, including DNA yield and fragment size, as well as post-capture sequencing metrics (Q30 > 90%, mapping rates > 95%, on-target rates 85–90%). The duplication rate was reduced to 5–8%, compared with 10–15% for manual methods, indicating increased library complexity. Bioinformatic evaluation of inter-species read mapping showed minimal cross-contamination, with a maximum contamination ratio of 0.0003%, indicating effective sample isolation in the automated workflow. High concordance in variant detection was observed between automated and manual workflows. Overall, this automated workstation provides a standardized and reproducible workflow that supports scalable precision genomics applications.

Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive21 in National Genomics Data Center22, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA017097) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human.

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Funding

This study was supported by Nanodigmbio (Nanjing) Biotechnology Co.Ltd.

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Authors and Affiliations

  1. Nanodigmbio (Nanjing) Biotechnology Co.Ltd., Floor 5-6, Tower 11, 71 XingHui Road, Jiangbei New District, Nanjing, Jiangsu, China

    Wenlong Xie & Chen Yang

  2. Nanjing Institute of Metrological Supervision and Testing, No. 10, Maqun Avenue, Qixia District, Nanjing, Jiangsu, China

    Shibo Ren

  3. School of Basic Medical Sciences, Yichun University, Yichun, China

    Wenlong Xie

Authors

  1. Wenlong Xie
  2. Chen Yang
  3. Shibo Ren

Contributions

Conceived and designed the experiments: Y.C., R.S., X.W. Performed the experiments: Y.C., X.W. Analyzed the data: Y.C., X.W. Wrote the paper: Y.C., R.S., X.W.

Corresponding authors

Correspondence to Chen Yang or Shibo Ren.

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Competing interests

The authors declare no competing interests.

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Cite this article

Xie, W., Yang, C. & Ren, S. Systematic performance evaluation and application validation of an end-to-end NGS workstation. Sci Rep (2026). https://doi.org/10.1038/s41598-026-43941-7

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  • DOI: https://doi.org/10.1038/s41598-026-43941-7

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