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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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The virus identified by genomad weren't annotated as virus sequence by VIBRANT? #99

Open Caiyulu-818 opened 1 month ago

Caiyulu-818 commented 1 month ago

The viruses identified by genomad weren't annotated as virus sequence by VIBRANT? Hi, when I input the virus sequences identified by genomad to identify AMG genes by VIBRANT(1.2.1), there wasn't any virus sequence, and also AMG genes annotated by virbant?

how can I deal with my results? which can I use in my analysis?

Best regards

apcamargo commented 1 month ago

Hi @Caiyulu-818

There can be several reasons for this. My first guess is that these are viruses that are missed by VIBRANT (which tends to have a lower sensitivity, as shown in geNomad's paper benchmarks). Can you provide more information? It would be useful to know the length of these sequences (as VIBRANT excludes short sequences from classification) as well as their CheckV estimates.

Caiyulu-818 commented 1 month ago

Hi, Thanks for your attention~These virus sequences were identified from MAGs by genomad, and I filtered and retained the virus sequences with length >2kb for the subsequent analysis, such as AMG annotation by DRAM. Best regards, lucy

apcamargo commented 1 month ago

Ok, so you allowed short sequences. That could explain why VIBRANT is not detecting many of them.

As far as I remember, VIBRANT uses KEGG orthologs to annotate AMGs. You can do your own KEGG annotation using a tool like PyKofamSearch.