PathoFact for metagenome assembled genomes (MAGs)
I am quite new to the analysis of virulence factors and antimicrobial resistance genes, and I have been looking for a suitable tool to search for these genes also in MAGs. Your tool looks very promising. If I understood your approach correctly, PathoFact takes as input the assembly (i.e. contigs) and the predicted ORF before the binning step. Would it also be possible to run PathoFact on the binned genomes (MAGs)? Would the performance of the tool be reduced by having less complex input (i.e. MAGs instead of the full metagenome assembly)?
Thanks a lot for your advise!
Kind regards, Christiane