RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data
Background The capacity of metagenomic sequencing-based diagnostics to fully identify infections have made them useful instruments in clinical practice. We introduce an interactive platform that runs on a local server-class hardware resource and implements a number of open-source programs. Results R...
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| Format: | Article |
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PeerJ Inc.
2025-08-01
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| Online Access: | https://peerj.com/articles/19849.pdf |
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| author | Jing Zhou Yao Tian Min Yang Ting Hao Jun Ma Shengyu Wang |
| author_facet | Jing Zhou Yao Tian Min Yang Ting Hao Jun Ma Shengyu Wang |
| author_sort | Jing Zhou |
| collection | DOAJ |
| description | Background The capacity of metagenomic sequencing-based diagnostics to fully identify infections have made them useful instruments in clinical practice. We introduce an interactive platform that runs on a local server-class hardware resource and implements a number of open-source programs. Results RpNGS integrates an interactive tabular interface for the management of experimental processes, patient metadata, and automated sequencing analysis. This technology optimizes clinical reporting by autonomously generating standardized reports in Word format. We have utilized the platform on an artificial microbial community reference panel and several clinical metagenomics datasets from public databases to demonstrate the efficacy of this workflow. Conclusions RpNGS is an innovative, user-friendly standalone application designed to store laboratory data (including reagents, primers, contaminants and run configurations), manage clinical metadata, process FASTQ files and produce analytical and comparative reports (including Word documents) that can be readily reviewed and certified. Its interactive interface necessitates no programming expertise, rendering it an invaluable instrument for clinical metagenomic pathogen identification. |
| format | Article |
| id | doaj-art-c93ee46d0cfe4debba1fb0355d4f142e |
| institution | Kabale University |
| issn | 2167-8359 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj-art-c93ee46d0cfe4debba1fb0355d4f142e2025-08-20T04:01:03ZengPeerJ Inc.PeerJ2167-83592025-08-0113e1984910.7717/peerj.19849RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics dataJing Zhou0Yao Tian1Min Yang2Ting Hao3Jun Ma4Shengyu Wang5Department of Intensive Care Unit, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, ChinaDepartment of Intensive Care Unit, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, ChinaDepartment of Intensive Care Unit, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, ChinaShaanxi Lifegen Co., Ltd, Xi’an, Shaanxi, ChinaShaanxi Lifegen Co., Ltd, Xi’an, Shaanxi, ChinaDepartment of Intensive Care Unit, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, ChinaBackground The capacity of metagenomic sequencing-based diagnostics to fully identify infections have made them useful instruments in clinical practice. We introduce an interactive platform that runs on a local server-class hardware resource and implements a number of open-source programs. Results RpNGS integrates an interactive tabular interface for the management of experimental processes, patient metadata, and automated sequencing analysis. This technology optimizes clinical reporting by autonomously generating standardized reports in Word format. We have utilized the platform on an artificial microbial community reference panel and several clinical metagenomics datasets from public databases to demonstrate the efficacy of this workflow. Conclusions RpNGS is an innovative, user-friendly standalone application designed to store laboratory data (including reagents, primers, contaminants and run configurations), manage clinical metadata, process FASTQ files and produce analytical and comparative reports (including Word documents) that can be readily reviewed and certified. Its interactive interface necessitates no programming expertise, rendering it an invaluable instrument for clinical metagenomic pathogen identification.https://peerj.com/articles/19849.pdfClinical metagenomicsWeb appPathogen detectionMetagenomic diagnosticsNext generation sequencing |
| spellingShingle | Jing Zhou Yao Tian Min Yang Ting Hao Jun Ma Shengyu Wang RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data PeerJ Clinical metagenomics Web app Pathogen detection Metagenomic diagnostics Next generation sequencing |
| title | RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| title_full | RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| title_fullStr | RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| title_full_unstemmed | RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| title_short | RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| title_sort | rpngs an automated platform for pathogen identification and monitoring in clinical metagenomics data |
| topic | Clinical metagenomics Web app Pathogen detection Metagenomic diagnostics Next generation sequencing |
| url | https://peerj.com/articles/19849.pdf |
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