Where Should I mention my refrence genome in PGAP pangenome analysis Command line ???
Dear all, If you are PGAP user help me, I have started to do Pangenome analysis with help of PGAP on my 5 strains from same species with one reference genome (PA01). Here, my doubt is, how can I compare my all 5 strains against reference genome. Thanks in advance.
Command Line : perl PGAP.pl -strains 2808+25832+28923+36155+38529 -input ../check/ -output ../result/ --cluster --pangenome --variation --evolution --function -method MP
In the command line -strains 2808+25832+28923+36155+38529 are my strains......Where should I mention my Reference genome in the command line??????????
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