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Peel, Ned, Martin, Samuel, Heavens, Darren, Yu, Douglas W. 
ORCID: https://orcid.org/0000-0001-8551-5609, Clark, Matthew D. and Leggett, Richard M.
(2025)
Real-time analysis and visualization of nanopore metagenomic samples with MARTi.
Genome Research, 35 (11).
pp. 2488-2500.
ISSN 1088-9051
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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.
| Item Type: | Article |
|---|---|
| Additional Information: | Software availability: The latest version of the MARTi software is available from GitHub (https://github.com/richardmleggett/MARTi) under the MIT License. A snapshot of the MARTi source code has also been included as Supplemental Code. Documentation can be found at https://marti.readthedocs.io/en/latest/. Additionally, an installation-free demo of the MARTi GUI is available at https://marti.cyverseuk.org/. The simulated reads used in this study, including both the full-length and one-third length data sets, are available at Zenodo (https://doi.org/10.5281/zenodo.14260487). |
| Uncontrolled Keywords: | genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1311 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Organisms and the Environment |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 10 Aug 2026 15:03 |
| Last Modified: | 10 Aug 2026 15:03 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/104095 |
| DOI: | 10.1101/gr.280550.125 |
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