Bioinformatics - Prokaryote Pan Genome with Roary! (Timestamps)

Happy start to the holiday seasons everyone! Today I am doing a quick look at Roary - the Pan Genome Pipeline. I briefly go over what I have found and done in a short exploration of the tool.

For Roary, I found out the need to install it a different way than typical `conda install -c bioconda roary`. The way that allowed Roary to actually function is `conda install -c bioconda/label/cf201901 roary".

00:12 New Shiny App???
00:51 What is Roary?
03:57 Retrieving genome assemblies
06:35 Setting up the conda environment
07:14 conda install -c bioconda prokka
08:06 Creating "genome.txt" for use with `parallel`
10:03 Running Prokka
14:21 Install Roary (conda install -c bioconda/label/cf201901 roary)
16:13 Running Roary
19:38 Roary output
21:00 roary_plots.py (https://github.com/sanger-pathogens/Roary/blob/master/contrib/roary_plots/roary_plots.py)
23:54 Installing dependencies for roary_plots.py
25:01 Viewing roary_plots.py figures
27:20 Pangenome Matrix explanation
28:26 Genes vs Genomes plot
30:00 Interactive Tree of Life

Links mentioned in the video -
Roary: the Pan Genome
https://sanger-pathogens.github.io/Roary/

Roary Pangenome Tutorial Documentation:
https://github.com/microgenomics/tutorials/blob/master/pangenome.md

NCBI Assembly:
https://www.ncbi.nlm.nih.gov/assembly

roary_plots.py
https://github.com/sanger-pathogens/Roary/blob/master/contrib/roary_plots/roary_plots.py

Interactive Tree of Life:
https://itol.embl.de/upload.cgi

DBGenerator.py
https://github.com/EnzoAndree/tutorials/blob/patch-1/DBGenerator.py
The image at the bottom left of the thumbnail is modified from AllGenetics.EU. Please consider contributing to my Patreon where I may do merch and gather ideas for future content:
https://www.patreon.com/AlexSoupir

Видео Bioinformatics - Prokaryote Pan Genome with Roary! (Timestamps) канала Alex Soupir