We have been using EPI2ME a lot lately and want to learn more about the new features. Tonight, I watched Sirisha Hesketh, Clinical Bioinformatician from Oxford Nanopore Technologies, present “EPI2ME everywhere” at London Calling 2024. They began with an overview of the workflows available: seventeen ranging from base calling and alignment to single-cell genomics. An upcoming workflow is wf-trio. EPI2ME workflows can be run on the cloud using the EPI2ME application or… using the command line. All workflows have fully featured HTML reports. Hesketh shared the wf-metagenomics workflow report with interactive plots and a complete version listing the tools used. IGV has now been integrated. Jupyter notebooks will be re-introduced to analyze data. Third-party workflows will be available by providers. The user interface will be improved, and I wonder when those updates will be released. Hesketh shared three examples of users: scientists sharing data, researchers in constrained IT environments, and researchers in the field. To address this, 2ME files will be bundled workflows that can be easily shared with collaborators. Later this year, users will be able to drag and drop 2ME files. Hesketh spoke about “bringing the analysis to the sequencer,” as in the case of automation with TurBOT. They explained that the NO-MISS bacterial genome analysis workflow is now available and the plasmid and 16S workflows will be released soon. AWS cloud-based compute options with EPI2ME will be publicly released later this summer. I have been fortunate to have early access and ran several EPI2ME Cloud analyses as part of the Portable Genome Sequencing course this spring. Hesketh noted that they plan on integrating EPI2ME with MinKNOW and devices used by core facilities, such as the GridION. With every update and EPI2ME video, I learn more about potential uses. I need to learn more about the Jupyter notebook options!
