Jimmy Creith is a Field Applications Scientist in bioinformatics. They work with Oxford Nanopore Technologies and presented the London Calling 2024 Masterclass I watched tonight. The session title was “How to analyse your data with EPI2ME.” We will use EPI2ME in the course. Creith focused on how EPI2ME can be used for small and large genome assemblies, including metagenomes. They also provided information about variant calling. Creith explained that EPI2ME can be run locally, on the cloud, or using a server. EPI2ME is fully supported and has a desktop application. A full cloud release is expected this year. EPI2ME produces full reports and corresponding files. EPI2ME uses Nextflow and comes with several available workflows. The software uses Docker. Sequencing and base calling can be done with MinKNOW. Then, EPI2ME can be used to run pre-configured workflows. Creith explained that EPI2ME has an alignment workflow that provides BAM files and a quality control report. For targeted sequencing, the wf-amplicon can be run de novo or against a reference. EPI2ME has several human genomics tools. The human variation and a cancer tumor-normal comparison can be used for variation analysis and methylation. EPI2ME offers a dedicated single-cell workflow for several kits, including spatial transcriptomics. The transcriptomics workflow can be used for cDNA or native RNA analysis. A reference is used to perform differential expression analysis. The plasmid assembly workflow produces a consensus fasta file for microbial genomics and can even compare inserts. For bacterial genomes, assembly and alignment (when reference is available) can be performed. The wf-metagenomics can be run in real time or post-run. By default, the workflow uses the NCBI database (16S, for example). There is a flu workflow to identify influenza A and B. The workflow concatenates reads, aligns, calls variants, and provides assignments. The ARTIC workflow is used for SARS-CoV2 analysis. There is a Mpox genome assembly workflow. There is a tuberculosis antibiotic resistance analysis workflow, too. The Pore-C workflow can improve assemblies and analyze chromatin structure from Pore-C library prep. Advanced tools include Modkit to work with modified bases and Medaka to create consensus sequences (Based on neural networks). The Nanopore Community releases analysis tools to further extend functionality. Creith demonstrated the use of EPI2ME for variant calling. A karyogram is created with areas of structural variation! The HTML report can be used to customize graphs, save graphs as images, and document versions of the software used. Creith recommended assessing the read length and depth needed for analysis. This session will be useful to share with students in the course.
