Tonight, I watched the London Calling EPI2ME product demo: “EPI2ME: democratising bioinformatics—from point-and-click analysis to custom integrations.” Natalia Garcia, a Bioinformatics Workflow Developer with Oxford Nanopore Technologies, explained how workflows use Nextflow and Docker containers. Seventeen workflows were available at the time of the recording during London Calling. Workflows can be run via the command line or EPI2ME desktop application. I had not considered and wondered if we should use EPI2ME via the command line. The new interface will include an integrated genome visualizer. Jupyter notes will be available in the app. Another upcoming feature is the inclusion of third-party analyses. Garcia shared that another feature is the use of workflows offline! Users can create their own workflows with a template that ONT provides. Chao Chun Liu, a Ph.D. candidate and bioinformatics consultant for Prarie Diagnostic Services, presented a short session titled “SamnSero: Real-time Bacterial Whole Genome Analysis.” The SamnSero workflow was designed as part of a diagnostic lab from Canada. The application was serotype analys of Salmonella. Liu demonstrated how to import the workflow. The pipeline can be used to expect sequencing data in a folder. Quality control options can be selected, and a Centrifuge database is needed. Genome polishing can be enabled. Liu used the GridION to base call data that was “fed” to the folder monitored by the pipeline. The data for the demo was from a Flongle with native barcoding. Liu switched on barcode trimming “for convenience,” and I would like to learn more about this decision. In real time, the report is generated per barcode. The pipeline performs genome assembly, classification, and reporting. The microbial composition of the samples is shown along with genome assemblies and serotype results for Salmonella. I visited the SamnSero GitHub page to learn that MAG binning is currently under development. I want to learn more about this workflow and try it!
