RT Journal
A1 Peel, Ned
A1 Martin, Samuel
A1 Heavens, Darren
A1 Yu, Douglas W.
A1 Clark, Matthew D.
A1 Leggett, Richard M.
T1 Real-time analysis and visualization of nanopore metagenomic samples with MARTi
JF Genome Research 
JO Genome Research 
YR 2025 
FD November 01 
VO 35 
IS 11 
SP 2488 
OP 2500 
DO 10.1101/gr.280550.125 
UL http://genome.cshlp.org/content/35/11/2488.abstract 
AB 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.