Maximum Contig Size for MOB-recon?

[schorlton]

Thanks for the great software! I'm wondering if the --max_contig_size param is implemented?

mob-suite/mob_suite/mob_recon.py

Lines 63 to 65 in 1d735b3

	parser.add_argument('--max_contig_size', type=int, required=False,
	help='Maximum size of a contig to be considered a plasmid',
	default=310000)

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):

mob-suite/mob_suite/mob_recon.py

Lines 66 to 68 in 3931722

	parser.add_argument('--max_plasmid_size', type=int, required=False,
	help='Maximum size of a reconstructed plasmid',
	default=350000)

[jrober84]

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]

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]

Ah ok, understood!