Outlook

If you are further interested in working with Nextstrain, you can check out the SARS-Cov2 Tutorial and go on with some steps, for example customizing your analysis or visualisation:

https://nextstrain.github.io/ncov/

And if you are totally enthusiastic about Nanopore data, you can do the course of last year, where we analysed two bacterial genomes. The course is still available online and you could follow the instructions. In some cases, the mapping tools used are not installed in your VM, then just use Minimap2 or BWA (depending on the data) and use GenomeView instead of IGV. We can’t guarantee that everything works exactly as last year, since some tool versions also changed. You can find the tutorial here:

https://denbi-nanopore-training-course.readthedocs.io/en/latest/