plasmid/chromosome/virus Classification problem

[darwin4442]

Hello if I want to find out from my metagenomic data whether each contig is the result of plasmid/chromosome/virus, do you have a recommended method? Can I directly use *aggregated_classification results

[apcamargo]

If you need every single contig to have a classification, you can use the aggregated classification results

[darwin4442]

Hello, I still want to confirm that *aggregated_classification results are reliable for chromosome/plasmid/virus classification Because I get the number of viruses and plasmids in _modified_virus_summary and SP1_modified_plasmid_summary under the *_modified_summary folder Are far less than the results predicted by *aggregated_classification results. For example, 317375 contigs predicted by *aggregated_classification results were viruses, 81229 contiGs were plasmids, But I finally *_modified_summary the results of viruses and plasmids only 1997 and 4334 contig, respectively...

[apcamargo]

That's because a few filters are applied after the classification itself to provide more reliable results. You can read more about it here.