How to handle plasmids?

[ammaraziz]

@gokeson Could you provide advice on how the pipeline should handle plasmids? In a test run I detected a 7.5kb plasmid, full length!

[gokeson]

Brilliant question. Most people tend to exclude the plasmid from the phylogeny tree. We can be smart and have two trees: one for the plasmid to show plasmid evolution and the other for the chromosome.

[ammaraziz]

We'll need a way to separate the plasmid sequence from the core genome of Ct.

Not sure how to handle this in the pipeline at this moment. There's a few options:

1. Annotate everything, then parse out the contigs annotated with plasmid or similar - not sure how this will go because plasmid annotations could be unpredicatable
2. blast for dnaA/repA to detect replication gene then pull out
3. something else?

[gokeson]

The best way is BLAST and pull. This is what I do manually anyway.

[ammaraziz]

What blastdb do you use?

[gokeson]

Sorry, I do my blast in genious without any db of mine. I can curate a db and send it over tomorrow