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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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[Question] Could MOB-suite be used in metagenomics data #144

Closed llk578496 closed 1 year ago

llk578496 commented 1 year ago

Hello! We have some Nanopore sequencing data for investigating urban metagenomics. We would like to find out the associations between mobile genetics elements and AMR genes. May we ask if MOB-suite could be used in this case?

Thanks a lot!

Eddie

jrober84 commented 1 year ago

It is not recommended to use MOB-recon on metagenomics since a key assumption it makes is that there is only one version of a mob-cluster present. This would likely cause plasmids which have multiple versions assembling of the MOB-cluster failing to get classified or a jumbled mess of contigs. You can definitely use MOB-typer on the reconstructed contigs you get from another software. We are contemplating extending functionality for plasmids in metagenomes but that is not something we have the resources to work on at present.