Circos workshop: plot genome alignments from scratch

This is a (hopefully comprehensive) description of a Circos demo that I gave for the Amsterdam Science Park Study Group on April 3rd, 2018.

Circos_demo_03-04-2018.ipynb
In this demo we align the genomes of two closely related Fungi, Fusarium graminearum and Fusarium oxysporum. We start really from scratch: we download the genomes from genbank, we align them using MUMmer, we write python scripts to generate karyotype-, link- and config-files used by Circos.

Circos_output_config_files.ipynb
This a little detour in the demo to show how Circos uses config files. I decided to leave it out of the main demo because I think it's next level. However, if you want to reach this level: check it out.