Possible to run progressive cactus with short viral genomes

[dduchen]

Hello,
I'm interested in progressively assembling a pangenome graph comprised of >500 viral genomes from the same family, but from many different species. These viruses are short (3-5kb) so I've been running into some problems getting progressive cactus to finish and am unsure what parameters I need to change (or whether the lengths of these genomes contraindicate using progressive cactus at all - which I know was developed with longer sequences in mind). Any suggestions on things to look out for or changes I could make to enable running this tool would be greatly appreciated.

Thank you!

[glennhickey]

There aren't many details to go on here, but progressive Cactus is indeed designed more for larger genomes. Still, I'd expect it to run fine on 500 viruses.