Individual cell analysis is possible with Oxford Nanopore Technologies (ONT). Matt Parker from ONT spoke about “Individual cells matter – single-cell data analysis with EPI2ME.” EPI2ME cloud was launched, and cloud-based analyses are possible. I have been testing and mentioning the new version in the Portable Genome Sequencing course. Bryan Leland, a Bioinformatics Manager with Oxford Nanopore Technologies, explained how long reads can improve transcriptomics. Fusion gene identification and isoform switching are possible. Single-cell RNA improves cell type identification, noted Leland. With PromethION flow cells, an output of 100M reads per flow cell is possible. This allows for plenty of cells to analyze per experiment. The EPI2mE wf-single-cell pipeline is described as an “end-to-end” pipeline that can be run on the desktop application or via the command line. This workflow generates detailed quality control data, raw output files, and key visualizations (and UMAPs!). Leland ran a live demonstration of the EPI2ME application updates and launched a run. If you run on the cloud, sequence files are uploaded. The cloud analysis will make EPI2ME more accessible to students in courses.
