Hello,

I want to use pggb (the pan genome graph builder) for pan genome construction. I am using:

pggb -i concatenated.fasta.gz -s -K -p -a -n -t  -v -l out

concatenated.fasta.gz file is made from merging two fasta files that I want to use for pan genome construction. I think this is not the correct way as the software treats same concatenated file both as a reference and a query. I also tried:

pggb -i file1.fasta.gz file2.fasta.gz -s -K -p -a -n -t  -v -l out

But then the software treats file1.fasta.gz both as a reference and a query.

I want to figure out what is the correct way to use multiple input files for this. Should the files be merged or input individually? Thank you!