These are chat archives for dereneaton/ipyrad
clust_thresholdis the sequence similarity of the regions which are overlapping.
query_covis how much of the sequence must be overlapping. Specifically, I think, how much of the query sequence must be overlapping with the target (seed). In PE ezrad it is likely that a low overlap (partially overlapping contigs) could cause a problem, tho I thought we had that working pretty well. It also seems reasonable that PE ezrad could have a very high htemp, but that shouldn't cause a crash... @Cycadales, The PE ezrad data should definitely be checked for adapters in step2, since the very common cutters used in that method often lead to adapter contamination.