Plasmid rotation?

[erinyoung]

I have issues with circlator, and was hoping to use dnaapler instead.

For plasmids, circlator uses prodigal to detect a gene somewhere in the middle and rotates the sequence to that. Does dnaapler do anything similar or does it just look for dnaA?

[gbouras13]

Hi Erin,

At the moment it doesn't. Dnaapler is a bit of just hack code I wrote really, it's not quite done!

I've had a bit of interest in dnaapler the last couple of days, so given that I am planning on making it a more usable when I get some time (bug fixes, new features, bioconda etc).

I think the best thing to do here is to implement what Ryan Wick did in Unicycler and use a repA database. Or alternatively the user can specify dnaapler choosing a random gene as you suggest.

George

[gbouras13]

Hi @erinyoung ,

I'm closing this now - I've implemented such functionalities with dnaapler plasmid and dnaapler mystery.

If you have any other comments please let me know

George

[erinyoung]

Thank you!