NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data

• Published in: Computational and structural biotechnology journal Vol. 20; pp. 5350 - 5354
• Main Authors: Rodríguez-Pérez, Héctor, Ciuffreda, Laura, Flores, Carlos
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.01.2022; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: adults; bioinformatics; biotechnology; cost effectiveness; genes; Internet; Microbiome; mortality; Nanopore; nanopores; patients; Pipeline; prediction; Real-time; Sequencing; ONT; Real-time; ROC; ICU; NGS; Nanopore; Sequencing; AUC; Pipeline; Microbiome
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2022.09.024

[Display omitted] The study of microbial communities and their applications have been leveraged by advances in sequencing techniques and bioinformatics tools. The Oxford Nanopore Technologies long-read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays. While this opens the possibility of sequencing applications outside specialized environments and real-time analysis of data, complementing the existing efficient library preparation protocols with streamlined bioinformatic workflows is required. Here we present NanoRTax, a Nextflow pipeline for nanopore 16S rRNA gene amplicon data that features state-of-the-art taxonomic classification tools and real-time capability. The pipeline is paired with a web-based visual interface to enable user-friendly inspections of the experiment in progress. NanoRTax workflow and a simulated real-time analysis were used to validate the prediction of adult Intensive Care Unit patient mortality based on full-length 16S rRNA sequencing data from respiratory microbiome samples. This constitutes a proof-of-concept simulation study of how real-time bioinformatic workflows could be used to shorten the turnaround times in critical care settings and provides an instrument for future research on early-response strategies for sepsis.