Real-time analysis and visualization of nanopore metagenomic samples with MARTi
- Ned Peel1,
- Samuel Martin1,
- Darren Heavens1,
- Douglas W. Yu2,3,4,
- Matthew D. Clark5 and
- Richard M. Leggett1,4
- 1Earlham Institute, Norwich, NR4 7UZ, United Kingdom;
- 2University of East Anglia, Norwich, NR4 7TJ, United Kingdom;
- 3Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China 650201;
- 4Centre for Microbial Interactions, Norwich, NR4 7UG, United Kingdom;
- 5Natural History Museum, London, SW7 5BD, United Kingdom
Abstract
The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.280550.125.
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Freely available online through the Genome Research Open Access option.
- Received February 14, 2025.
- Accepted September 26, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.