Hi Isaac, thanks for the quick reply and clarifications. My data is single-end, but I guess the 2-4 values separated by comma(s) are needed nevertheless, at least for some of the parameters. For instance, for the edit_cutsites parameter, I get an error if I try using "TGCAT" instead of "TGCAT, 0": "Error setting parameter 'edit_cutsites'; list index out of range; You entered: TGCAT". Runs fine if I add ", 0". But the data are single-end, so not sure what ipyrad is doing with the parameter stated like that. As for the trim_overhang, I was getting an error - I'll try it again and see if it persists. Thanks!