Tonight I watched the London Calling 2023 product demo for “Analysing bacterial genomes – from species identification to AMR.” Stephen Rudd, Director of Bioinformatics Product at Oxford Nanopore Technologies (ONT), shared their work on EPI2ME labs products. They have been developing EPI2ME Labs workflows for several years. These are pre-installed workflows that can help solve different biological problems. There are workflows for human genome variation, alignments, and microbial genomics. The EPI2ME Labs team is working on cloud-based computing options. The demo shared how the metagenomics workflow is run on the cloud. Natalia Garcia, a Bioinformatics Workflow Developer, explained how this pipeline can be run by simply setting a path to the samples (FASTQ files), options for taxonomic assignment (Kraken2 or minimap), and default databases or custom ones. You can also customize memory and CPU use. The report is similar to the existing EPI2ME Labs metagenomics reports: interactive quality control and lineage plots are available. It is also possible to now compare samples! Tables can be exported as .CSV files. Alpha diversity and species richness values are calculated. The workflow can be run on the device, on the cloud, and near real-time! Matt Parker, Associate Director of Clinical Bioinformatics with ONT spoke about the workflow for detecting genes present in a bacterial isolate. You can specify a reference and ResFinder is an option to find point mutations for some species. HTML reports can be shared with collaborators. The report has read quality, length, and base yield over length. Assembly statistics including circular contigs (plasmids) and coverage is displayed. Annotation is displayed as a table. Antimicrobial resistance genes and, if available, point mutations contributing to resistance are displayed. The advantage is that the workflow can be run in the cloud. I do hope we are able to use this workflow with students!
