search

AnantharamanLab / vRhyme

Binning Virus Genomes from Metagenomes
GNU General Public License v3.0
55 stars 9 forks source link

Regarding dereplication of bins #10

Open ShailNair opened 1 year ago

ShailNair commented 1 year ago

Hi, Thanks for the excellent tool. I did binning using vRhyme and PHAMB (VAMB) tools. Next, I want to combine the bins from these two packages into a new non-redundant set. Can I use the dereplication option of vRhyme to do this? If not, do you have any suggestions regarding this aspect?

Thank you

KrisKieft commented 1 year ago

The built in dereplication mode for vRhyme isn't necessarily built for combining bins. dRep can dereplicate bins into a non-redundant set, but it doesn't combine to my knowledge. DASTool will combine microbial bins but I think it's dependent on microbial single copy genes. There may not be a best option at the moment. Are you more interest in combining or just dereplicating? The easiest way would be to pick one bin representative instead of combining.

ShailNair commented 1 year ago

Yes. combining is a problem with viral bins. I used the dRep tool to pick a representative bin based on ANI similarity, contig length, and N50. Although this isn't the best option, I didn't find any other alternative.

KrisKieft commented 1 year ago

I don't really have any better alternatives. Maybe the viral group at JGI has a tool in the works.

ShailNair commented 1 year ago

That sounds great. hope it comes out soon. Thanks.