Modified Geneious assembly parameters: Allow Gap X Maximum Per Read = 15% Minimum Overlap = 60 Word length = 14 Ignore words repeated more than WAS NOT CHECKED Maximum Mismatch Per Read = 30% Maximum Gap Size = 5 Minimum Overlap Identity = 95% Index word length = 14 Reanalyze threshold = 0 Maximum ambiguity = 16 Don’t merge contigs when there is a variant with coverage over approximately WAS NOT CHECKED