Antônio Camargo

Hi @rpetit3 I wouldn't, but I think it would be too much of an overhead just for this

Hi @xjhzjucas You can use the realm-level classification to infer the Baltimore classes: - *Duplodnaviria*: dsDNA - *Varidnaviria*: dsDNA - *Monodnaviria*: ssDNA - *Riboviria*: Multiple types of RNA virus. You...

You can find the AMR annotations of all input sequences in the `_annotate/_genes.tsv` file. Genes with AMR annotation will be indicated in the `annotation_amr` column.

Thanks again for your input, @LanderDC! Regarding the NCBI changes, these will only affect species names, not higher taxa. As far as I recall, all higher taxa from ICTV are...

I misread your code. I though you were running geNomad on a concatenated FASTA (which wouldn't make any sense). You're right that calibration probably won't work well on single genomes...

Hi @songmj86 > "provirus_3961739_3974913" is free of integrase. Can we call it prophage? Not having an integrate detected by geNomad doesn't mean that the sequence is not a provirus. Several...