Roary pan genome tutorial | Bioinformatics tutorial on Pangenome analysis of bacterial genomes

A step-by-step process of performing pangenome analysis using the tools Prokka and Roary. On bacteria genomes

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Materials
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How to install anaconda
Linux    • Install , Configure and Run Anaconda in  a...  
MacOS    • How to Install and Run Anaconda in  MacOS ...   - GUI Installer
   • Install, Configure and Run Anaconda in ANY...   - Command line installer

Roary github page
https://github.com/sanger-pathogens/R...
python script:https://github.com/sanger-pathogens/R...

Data for the S.aureus strains can be downloaded from here
https://www.ncbi.nlm.nih.gov/nuccore/... V521 strain
https://www.ncbi.nlm.nih.gov/nuccore/... M48 strain
https://www.ncbi.nlm.nih.gov/nuccore/... P10 strain
https://www.ncbi.nlm.nih.gov/nuccore/... AR465 strain
https://www.ncbi.nlm.nih.gov/nuccore/... NRS1 strain
https://www.ncbi.nlm.nih.gov/nuccore/... R50 strain



Chapters
00:10 Outline
01:33 Explanation and importance of pangenome analysis
03:04 PC Requirement
04:02 Add conda channels
05:19 Create conda environment and install tools
06:36 Activate conda environment
07:15 Set working directory
07:57 Download roary_plot.py python script : https://github.com/sanger-pathogens/R...
09:40 Install python dependencies
13:44 Download genome sequences
17:31 Perform genome annotation using prokka
24:29 Perform pangenome analysis using roary
33:52 Roary output
34:04 Interpret results
34:09 Gene presence and absence file
36:19 Pangenome matrix
38:17 Pangenome pie chart






#bioinformatics #genomics #bioinformática #microbiology #datascience