Roye Rozov
Roye Rozov
Hi Ryan, I would also be very interested in this feature. I'm the developer of Recycler (https://github.com/rozovr/Recycler), which searches for graph cycles as potential plasmids, and being able to do...
Ryan, Thanks for the quick reply. I just wanted to second the vote in favor of .paths over .GFA. Also, I think Rayan's idea of having colored lines along the...
Hey Ryan, thanks for considering this. The second case is not clear to me - can you clarify why the two edges share the same overlap? I think there are...
For isolates, all our testing was done with default parameters of spades. For metagenomes, especially large ones, I would currently recommend Megahit. Again, we didn't use special parameters. I think...
This looks like a pysam related error. Please check pysam is installed properly.
Can you please me how you installed recycler? I.e., did you do git pull, download a zip, etc. and where from? That will help me diagnose why this happens.
@OAF12 and @sergiomorgado , sorry for my delay, am wrapping up my thesis now; will look into this soon
For cycles that are composed of multiple contigs in the graph, the second output file is meant for this purpose: .cycs.paths_w_cov.txt - a text file containing information about plasmids composed...
and no worries about the comparison
It looks like an installation problem - have you tried the non-bioconda install steps?