RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data

TL;DR

RpNGS is a user-friendly platform that automates pathogen identification and reporting in clinical metagenomics data.

Contribution

RpNGS introduces an automated, standalone platform for managing and analyzing clinical metagenomics data without requiring programming skills.

Findings

RpNGS integrates an interactive interface for managing experimental processes and patient metadata.

The platform generates standardized clinical reports in Word format automatically.

RpNGS was validated using an artificial microbial community and public clinical datasets.

Abstract

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.

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.

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.

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