Minimum length of scaffolds?

[MrOlm]

Hello,

I was wondering if there is a minimum length requirement for scaffolds somewhere hard-coded in the program?

I performed a test where I compared the length of genomes before running Panseq on them and after (by summing up all of the fragments each genome had in the Pangenome, as well as the length of the fragments). For the most part these numbers agreed very well (1-2% difference), but with highly fragmented genomes (with a lot of small pieces) there was as much as a 13% reduction in genome size.

The smallest scaffolds I used as input are 1kb, but I was wondering if I should make that even higher?

Thank you for the wonderful tool, -Matt