Antônio Camargo

I'd say those are most likely misbinned contigs. It is well known that [MGEs bin badly](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000436?crawler=true). As for the second question, you can interpret that as multiple infection events from...

Thank you for bringing this to my attention. This is an interesting case because it seems that at least a portion of the genes of this replicon are indeed of...

If you're not interested in viruses at all, you can just delete `_find_proviruses` directory and then run the end-to- end command with the `--disable-find-proviruses parameter`. No provirus will be detected...

From experience, PLSDB (or at least the previous version of it) had a couple of actual phages there (I couldn't find evidence of them being hybrid elements). This is not...

I just noticed that NC_016838 got a virus score higher than the plasmid score, so disabling provirus discovery won't help. I need to take a look at this manually. You...

Thanks a lot! This will be very helpful. I'll work on this soon and make a new release.

There is currently no option to do this, but I could implement it as a feature in the future. In the meantime, you can obtain the nucleotide sequences of the...

You can use [`taxopy`](https://apcamargo.github.io/taxopy/) for that. geNomad's taxdump is inside the database directory, and you can find the TaxIds in the `_annotate/_taxonomy.tsv` file. For instance: ```python import taxopy taxdb =...

"Unclassified" means that the genes in the sequence had no matches to markers with taxonomy information. "Viruses" means that the classification is uncertain at a high rank.

@gbouras13 are you using some sort of workaround for the time being? I wrote a [quick script](https://github.com/apcamargo/reorient-circular-seq) to deal with this issue, but I'm not a big fan of my...