Real-time metagenomics with MARTi

Richard presented MARTi (Metagenomic Analysis in Real Time),  a new real-time metagenomics software package developed by his team at the Earlham Institute, UK. He first described the origins of the software, which came out of previously published work (Nat. Microbiol. [2020]) investigating necrotising enterocolitis in pre-term babies – a condition associated with gut microbial dysbiosis (an increase in pathogenic bacteria and reduction in beneficial bacteria). Standard tests for this condition are slow, taking approximately 48 hours; however, using nanopore sequencing on the MinION, the team were able to reduce this to approximately 5 hours. Key to this work was the development of the software NanoOK RT, which carries out real-time pathogen and AMR analysis. Although a useful tool, Richard explained that NanoOK RT had a few limitations, namely a relatively heavyweight Java user interface, limited extensibility, and a suboptimal installation procedure. MARTi was developed to address these limitations. Richard shared a number of screenshots of the intuitive and customisable graphical user interface, displaying metagenomic data in a range of formats, including phylogenetic trees. AMR analysis results were also displayed. It is also possible to compare samples, simply by selecting multiple samples of interest. Richard described how all of the data plots can be exported as SVGs for use in other reports and publications. Furthermore, intermediate data can be downloaded as tab separated files for further downstream analysis. The platform is supported by most browsers and will adjust its display to suit the device it is running on, allowing its use on tablets if desired.

Richard then explained the workings of MARTi, which starts with importing basecalled FASTQ files from the nanopore sequencing device. The data is then prefiltered before being chunked for efficient processing. For classifying organisms, the software can optionally use BLAST or Centrifuge, with AMR analysis performed using the CARD database.

Richard pointed delegates to a server (http://marti.cyverseuk.org), where the software can be tested using existing data, and welcomed feedback on any features that users would like to see incorporated. A pre-print describing the software is also anticipated soon.