I faced with the following problem:
Building the tree takes too long due to the large amount of data I have. Now it takes a week to calculate it. And with each next week, the amount of data increases. (Now I have already 20k of subsampled samples, but soon it will be about 40-50k)
(I am still using the default parameters for Nextstrain. In other words, I haven’t changed anything in main_workflow.smk)
Is it possible to somehow optimise (or tune) some of the parameters in one of the .smk files to speed up the calculations?
Or maybe I can build a new tree not from scratch, but based on the previous one.
For example, I have my already built tree. I am getting a new data. Can I build a new tree with new data starting from the tree I already have?