Metagenomics—the study of all genetic material in a given environment—has become a cornerstone of modern biology, unlocking insights into microbial communities that shape everything from soil health to human disease. But until recently, the promise of real-time metagenomic analysis remained just that: a promise. Now, researchers at the Earlham Institute have developed a new tool to possibly transform that promise into reality.
Published in Genome Research and titled “Real-time analysis and visualization of nanopore metagenomic samples with MARTi,” the open-source software MARTi (Metagenomic Analysis in Real-Time) enables real-time visualization of metagenomic data generated via nanopore sequencing, with potential applications in detecting microbial threats across clinical, agricultural, and environmental settings.
“MARTi has its origins in software we developed for really rapid identification of pathogens in preterm infants,” said Richard Leggett, PhD, technology algorithms group leader at the Earlham Institute. “But we’ve since adapted it to use in a wide range of settings, including on board research vessels in the Antarctic, in agriculture, and in biosurveillance and security.”
At its core, MARTi consists of two components: the MARTi Engine, which performs the analysis and can run on anything from a standard laptop to a high-performance computing system; and the MARTi GUI, a web-based tool that lets users visualize results, compare datasets, and generate graphs and figures. It supports multiple classification methods—including BLAST, Centrifuge, and Kraken2—and allows researchers to customize parameters and databases to suit their needs.
“It’s operationally very lightweight,” said first-author Ned Peel, PhD, a postdoctoral research scientist at Earlham Institute. “You can use it in-field for taxonomic classification on a standard laptop, or undertake larger, complex analysis using high-performance computing.” That flexibility is especially valuable in time-sensitive scenarios—whether identifying pathogens in clinical samples or tracking antimicrobial resistance genes as they emerge.
Antimicrobial resistance (AMR) continues to challenge global health systems, making timely detection of resistance genes increasingly critical. MARTi’s browser-based interface offers real-time updates on microbial community composition and the presence of AMR genes.
Another application of MARTi is its integration with AirSeq, a technology developed by the Earlham Institute and the Natural History Museum, London. AirSeq captures and purifies trace DNA from air samples, which is then sequenced and analyzed using MARTi.
“One end-goal in agricultural settings would be to have a box in a farmer’s field that could continually sample the air, analyzing the data onboard with MARTi and then providing the farmer with an alert in real time,” added Leggett.
MARTi has already been deployed in multiple collaborations and tested on both simulated and real-world datasets, demonstrating performance in read classification, taxon detection, and relative abundance estimation. MARTi represents a major advance in the accessibility and functionality of real-time metagenomic analysis. It’s not just a tool—it’s a technological platform that may transform how we monitor and respond to microbial ecosystems.