Tonight I watched the EPI2ME updates from Matt Parker, Associate Director of Clinical Bioinformatics at Oxford Nanopore Technologies. We will use EPI2ME next week as part of the Portable Genome Sequencing course, focusing on bacterial genome assembly and metagenomics. This Nanopore Community Meeting Houston update started with a high-energy EPI2ME video highlighting updates to compute locally or in the cloud, integrate pipelines, and perform complex computational workflows. Parker explained that they want to make bioinformatics easy to use to address biological questions. Parker noted that the EPI2ME team designs state-of-the-art yet easy-to-use tools. Usability is an important aspect of EPI2ME. Parker spoke about building bioinformatics tools that work on Mac processors. There is an EPI2ME desktop application, and all the tools are deposited on GitHub. Their blog includes several articles about workflows and common analyses. Their catalog of workflows has several infectious disease and microbiology workflows. Inputs will now allow Bam files. The reports are very detailed and dynamic. Summaries can be used in downstream analyses. Parker explained that a new workflow provides information on vector construction for AAV vectors. A cloud backend is being developed for Amazon Web Services storage and computing power. Now, when you select a workflow, you can decide whether to run it locally or on the cloud. Parker said there are about twenty workflows available. You can also run demo files. “Sensible default” parameters are provided, and “power users” can change them. EPI2ME will continue to improve by including a connector between MinKNOW and EPI2Me. Parker explained that the AmPORE-TB workflow will quickly take samples to antimicrobial resistance reports. Third-party integrations will help users interpret data: Oxford Nanopore Technologies is partnering with others to offer in-depth analyses. In class, we will use EPI2ME to assemble genomes and analyze metagenomes!
