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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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Whether measures have been taken by genomad to avoid identifying genomic islands as viruses? #96

Closed ZongzhiWu closed 2 months ago

ZongzhiWu commented 2 months ago

Dear authors,

I wonder if any measures have been taken by genomad to avoid identifying genomic islands as viruses?

Thanks a lot!

apcamargo commented 2 months ago

Yes, geNomad shouldn't classify genomic islands as proviruses. The default cutoffs will remove those for you. If you want to be extra conservative, you may require proviruses to have a virus hallmark

ZongzhiWu commented 2 months ago

Will genomic islands be classified as plasmids or chromosomes in genomad?

apcamargo commented 2 months ago

This shouldn't happen. However, ICEs and plasmids can be very similar, so if your assembly is very fragmented and the chromosome regions flanking ICEs are absent, it is possible that they will be classified as plasmids

apcamargo commented 2 months ago

This shouldn't happen. However, ICEs and plasmids can be very similar, so if your assembly is very fragmented and the chromosome regions flanking ICEs are absent, it is possible that they will be classified as plasmids

ZongzhiWu commented 2 months ago

Thank you very much for your reply.