Roary and Phandango - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki

Roary is a pan-genome pipeline for calculating pan-genomes using a GFF3 files that can be generated using Prokka or GenBank. The basic steps to using Roary are:

• Annotate FASTA files with PROKKA
• Roary –e –mafft *.gff
• FastTree –nt –gtr core_gene_alignment.aln > my_tree.newick

However they do have a more indepth tutorial. The Roary Hompage does have a man page for every command with more details about their options if you wanted to take a look at that.

There are two options for visualizing your results from Roary. You can the website Phandango, or you can use roary_plots.py.

Roary does not come with this script automatically. You can find this file here. There is also a roary_plots.ipybn file, which is a python notebook file if you want an interactive tutorial. Otherwise just download the file from github by cloning Roary and going into the /contrib folder, or by copy and pasting into a new file. Then you are ready to run using python roary_plots newick_tree.newick presence_absence.csv.

Note: preferred browser is Chrome. This is really great for making a newick tree and a matrix with the presence and absence of core and accessory genes. Its also really easy to use, just drag and drop your "my_tree.newick" (or core_gene_tree.newick if you use default settings) file and your presence absence table "gene_presence_absence.csv" into the browser (at the same time). Press "p" to save the visual conveniently in an .svg file.

You can edit the .svg file with inkscape (free, open source). Inkscape has a steep learning curve, but once you know it, it is very powerful. The preferred image editor of many bioinformatics folks. ---JM

I took the phandango.svg and trimmed off a lot of the default features, so I had just the heatmap and tree. I then used inkscape to change font size/ color etc on my tree labels for meaningful metadata groups and added the bars that indicate the core/shell/cloud genes - with numbers from the "summary_statistics.txt" file from roary.