Happy Thanksgiving! Tonight I watched a second video on EPI2ME Labs that is part of the Human genome sequencing and analysis course offered by Nanopore Learning. This half-hour video presented by Bala Periaswamy from Oxford Nanopore spoke about EPI2ME Labs and how it can run workflows through the use of Docker and Nextflow. The wf-human-variation workflow takes signal data files or bam files from human genome sequencing experiments. They recommend starting with bam files with methylation tags since the files are more manageable. This workflow can identify single nucleotide variations. SNPs, SVs, and even copy number variation (planned as of recording of the video) information can be obtained from this workflow. Periaswamy demonstrated the workflow with subsampled data from chromosome 17. They were using a Linux laptop with multiple cores and 32 Gb RAM. The EPI2ME Labs homepage has several workflows that can be installed. Workflows are installed from the Github directory of ONT. Periaswamy recommended saving the data in a different working directory than home with sufficient space. The workflow has several parameters that can be modified as well as input file options. They recommend providing a bam file. The basecaller config file is required and has the settings for the basecaller model and kit used. This is because the variant caller does need the basecaller model. The structural variation calling options allow for the user to provide a tandem repeat annotation file that can improve variation calling. Files and sequences can be phased. Periaswamy warned that some of the options do generate large files. The workflow supports fast5 and pod5 files. Default settings auto populate and can be modified and saved as a Nextflow configuration file. For example, memory can be allocated for the workflow. The demo shared configuration and setup of a run and the output obtained. This workflow may change with the updates to EPI2ME an EPI2ME Labs. Nevertheless, it is useful to know this is available. I wonder if it can be modified to use an alligator or wax worm genome… I believe changes in EPI2ME and EPI2ME Labs will allow for more cloud-based analyses. The results of this workflow were visualized with the integrated genome browser. There is a track for SNV, for example.
