Matt Parker, the Director of Clinical Bioinformatics Software at Oxford Nanopore Technologies, facilitated the Nanopore Community Meeting Boston 2024 session on variant analysis with EPI2ME. The title of the presentation was “Ultra-rich human data – variant analysis with EPI2ME.” They shared the EPI2ME user interface updates that were recently released. There is a new element to the dashboard: resource use and storage space! I didn’t know storage space was included! Connection notifications are now enabled. The human variation workflow, for example, has a genome browser integration. Parker spoke about future updates that will allow the GridION to run workflows. They also mentioned the use of EPI2ME on HPCs. Sean McKenzie, Associate Director of Genomic Applications Bioinformatics, explained how long reads can help uncover variants. They described a set of tools that can be used with the variant analysis workflow available on EPI2ME. The Clair3 can call and phase SNVs. Phase blocks can be called and analyzed. Sniffles2 calls translocations, inversions, duplications, and large insertions/deletions. Spectre is a tool to call copy number variants based on read depth. The Dorado base caller can distinguish between canonical and modified CpGs. The methylation can be phased. Straglr is used to identify genotype phenotype-relevant STR repeats. The EPI2ME app can load the variant workflow. The user sets the options for the kinds of variants identified. The references and reads used are selected. The workflow can run on the cloud or locally. The reports produced are rich interactive HTML files. I don’t do variant analysis, but I want to explore this tool!
