Pangenome Analysis using Roary tool

Question

[User 3325]

How can I find core proteins (step by step) from 30+ strains data using roary pangenome analysis tool?

Answer 1

[konstantinkul]

Install Roary and Prokka
Go to path with fasta genomes
> cd path/to/fastas/
Annotate fasta genomes with Prokka
> for i in *.fa; do prokka $i --addgenes --locustag ${i%.*} --force --cpus 32; done
Collect all GFF files from each genome folder to tm folder
> mkdir tm && find . -name "*.gff" -type f -exec cp {} ./tm \;
 Copy files to roary folder
> cp path/to/tm/* path/to/roary
Run roary to produce core genome alignment
> roary -e --mafft -p 32 *.gff
Or just comparison
> roary -p 32 *.gff
If needed change the minimum blastp percentage identity. Its not advised to go below 90% unless you know what you're doing.
> roary –i 90 *.gff
Check the file gene_presence_absence.csv

[User 3325]

Thank you so much for detailed reply. I have all gff and I have already run this command roary -e --mafft -p 32 *.gff but I could not identify where genes/protein sequences/ID are generated for core genes. Can you help help me finding that. even in file gene_presence_absence.csv how to extract core one.

[konstantinkul]

Open file gene_presence_absence.csv in Excel and select all rows where 'No. isolates' equal to a number of analyzed genomes (strains). These genes will be core genes.

[User 3325]

Thank you so much now I got it.

[sarvaninram]

I am not able to follow this explanation,could you help on how to identify core genes from the presence absence file.

[jeccy.J]

Could you please explain how to extract the SNPs from the final output of Roary.