Hi!
First of all I would like to thank you for developing this toolkit to extract and annotate mitogenomes, I've been loving it and it's really intuitive.
Currently, I'm trying to extract mitogenomes from samples of unknown origin (mostly animal hair from ethnological collections, but also feacal extracted sequences) and trying to rebuild the mitogenome and detect its species. I am working with low depth and extremely low depth sequencing (sometimes as low as 0.1x) and I'm trying to figure out the best MitoFlex options (if there are any!) to extract even some discernable mitosequences.
I wanted to ask you what options you would suggest using. Currently, I'm trying with a depth list of 0s, and also trying with smaller kmers (17, 21, 25, 27), but I'm not getting great results. Would you disable filters altogether? Is my approach even feasible or am I just wasting time fighting windmills?
Hi! First of all I would like to thank you for developing this toolkit to extract and annotate mitogenomes, I've been loving it and it's really intuitive. Currently, I'm trying to extract mitogenomes from samples of unknown origin (mostly animal hair from ethnological collections, but also feacal extracted sequences) and trying to rebuild the mitogenome and detect its species. I am working with low depth and extremely low depth sequencing (sometimes as low as 0.1x) and I'm trying to figure out the best MitoFlex options (if there are any!) to extract even some discernable mitosequences. I wanted to ask you what options you would suggest using. Currently, I'm trying with a depth list of 0s, and also trying with smaller kmers (17, 21, 25, 27), but I'm not getting great results. Would you disable filters altogether? Is my approach even feasible or am I just wasting time fighting windmills?
Thank you Giacomo