Hello,

I have a few questions regarding the Verkko and the alignTips step:

1. I'm trying to assemble a very large genome of ~30 GB. Fortunately, verkko has behaved very well and assembled it without major issues. However, I did notice the alignTips step was taking particularly long, and upon checking the logs I realised that winnowmap was generating a multipart index since the genome size is bigger than 4G. I edited the -I flag locally to -I 40G, but it would be nice if it were set by default to a larger value or at least there was a command line option in Verkko to adjust it.
2. I don't understand why winnowmap is used without the high frequency K-mers counts file as input. If it's not provided, can it still align to highly repetitive regions? I assume the high frequency kmers are not downweighted but also not dropped if done this way?

Thanks a lot in advance for the clarifications!