{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T03:02:33Z","timestamp":1792292553025,"version":"4.4.0"},"reference-count":26,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T00:00:00Z","timestamp":1754956800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100017596","name":"Natural Science Basic Research Program of Shaanxi Province","doi-asserted-by":"crossref","award":["2021JQ-543"],"award-info":[{"award-number":["2021JQ-543"]}],"id":[{"id":"10.13039\/501100017596","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002858","name":"The China Postdoctoral Science Foundation","doi-asserted-by":"crossref","award":["2020M673605XB"],"award-info":[{"award-number":["2020M673605XB"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Scientific Research Foundation of Shaanxi University of Science and Technology","award":["2019BT-35"],"award-info":[{"award-number":["2019BT-35"]}]},{"name":"The Shaanxi Qin Chuang Yuan \u201cScientists + Engineers\u201d Team","award":["2022KXJ-011"],"award-info":[{"award-number":["2022KXJ-011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n               <jats:title>Background<\/jats:title>\n               <jats:p>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.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Results<\/jats:title>\n               <jats:p>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.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Conclusions<\/jats:title>\n               <jats:p>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.<\/jats:p>\n            <\/jats:sec>","DOI":"10.7717\/peerj.19849","type":"journal-article","created":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T08:41:46Z","timestamp":1754988106000},"page":"e19849","source":"Crossref","is-referenced-by-count":2,"title":["RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data"],"prefix":"10.7717","volume":"13","author":[{"given":"Jing","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Intensive Care Unit, The First Affiliated Hospital of Xi\u2019an Medical University, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Intensive Care Unit, The First Affiliated Hospital of Xi\u2019an Medical University, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Intensive Care Unit, The First Affiliated Hospital of Xi\u2019an Medical University, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Hao","sequence":"additional","affiliation":[{"name":"Shaanxi Lifegen Co., Ltd, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ma","sequence":"additional","affiliation":[{"name":"Shaanxi Lifegen Co., Ltd, Xi\u2019an, Shaanxi, China"},{"name":"Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangzhou, China"},{"name":"School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Intensive Care Unit, The First Affiliated Hospital of Xi\u2019an Medical University, Xi\u2019an, Shaanxi, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2025,8,12]]},"reference":[{"key":"10.7717\/peerj.19849\/ref-1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.7554\/eLife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"ELife"},{"key":"10.7717\/peerj.19849\/ref-2","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1093\/bioinformatics\/btz715","article-title":"Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen 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