w1bw
commented
5 years ago Sorry, cleaning out old Pilon support requests, and I see this didn't get a response. I have no experience using pilon with Dovetail or Hi-C, and the other library you mention has reads which are really short for use with Pilon (it won't be able to do local reassembly unless you set the K value to much less than your read length). Obviously this response is too late to be much help to you, but I would be interested in hearing how will different attempts worked.
Hello, I wonder if it will be OK using a Dovetail library (restriction enzyme-based) for polishing a Falcon (+ Quiver) assembly. I am aware that the reads will not be distributed uniformly: will the corrections made where there are alignments still be meaningful? it would be about 4-5x In alternative, I have a 5x of a WGS PE library (2x44 bp) and probably some data from Hi-C libraries. Which one would this be better, if any? Thanks, Dario