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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Maximum Contig Size for MOB-recon? #101

Closed schorlton closed 2 years ago

schorlton commented 2 years ago

Thanks for the great software! I'm wondering if the --max_contig_size param is implemented? https://github.com/phac-nml/mob-suite/blob/1d735b30053b45457a59c277c8d996ab86e0347c/mob_suite/mob_recon.py#L63-L65

I couldn't find it in the code if so. Just hit a case where we classified a complete circular 1+Mb bacterial genome as a novel plasmid. Thanks!

Addendum: also wondering about --max_plasmid_size (couldn't find it either): https://github.com/phac-nml/mob-suite/blob/39317225fcbd0a98fd1f1bd663d91932ae0fae8e/mob_suite/mob_recon.py#L66-L68

jrober84 commented 2 years ago

Thanks for pointing that out, yes both of those options were orphaned in the update, I have added back in their functionality as quality checks and they will be available in the new version. Very cool you are finding plasmids that size, I know Borellia can have large plasmids nearing that size.

schorlton commented 2 years ago

Thanks! *should not be finding plasmids that size - as per issue "we classified a complete circular 1+Mb bacterial genome as a novel plasmid" and I want to avoid this with the max size parameter!

jrober84 commented 2 years ago

Ah ok, understood!