These are chat archives for dereneaton/ipyrad
I'm looking at the args to smalt:
... -f sam -n 2 -x -c 0.85
it looks like these do the following:
-n = threads
-x = use exhaustive search
-c = minimum coverage of kmers to the query seq
Would we get better matches if we messed with these flags?
-m = minscor. default is <wordlen> + <stepsize> - 1.
-y = minid. This seems like the closest to vsearch clust_threshold.
Because at the moment it seems like we are missing ref matches by some sequences and not others in the sim data even when they only differ by one base.