Circos workshop: plot genome alignments from scratch
| Main Author: | Like Fokkens |
|---|---|
| Format: | info lesson Journal |
| Terbitan: |
, 2018
|
| Subjects: | |
| Online Access: |
https://zenodo.org/record/1220855 |
Daftar Isi:
- 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.