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How to understand the results? #6
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Hi @alienzj There are a couple of points here:
Aggregating the output of several classification tools is difficult because they will often diverge. geNomad is, in average, more accurate than VirSorter2 (see figure below), but VS2 is an amazing tool and I can't guarantee that geNomad will be correct in every single scenario they diverge. You should gather as much information as possible. The good news is that geNomad's output includes some information that makes it easier to understand why a given sequence was classified as a plasmid or virus: This is an example of a
Here you can see that these sequences encode plasmid hallmarks, which is a very good indication that those sequences are indeed plasmids. Try to check if your sequences also encode those. In addition, the The same is true for the Again, if you are only interested in the taxonomy, just look at Hope this helps! |
Dear @apcamargo, thanks a lot for your quick and detailed reply.
Thanks a lot again! |
Thanks @alienzj There are certainly lots of plasmids in your data. You can easily see that in the
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Hi, @apcamargo, Thanks a lot for your reply. It is quite interesting that find so many plasmids from the viral vMAGs identified by VirSorter2 and phamb. |
No problem! Let me know if you have more questions :) |
Dear @apcamargo,
thank you for developing so great tool!
I used it to do viral genome taxonomic assignment:
Here is the summary of results:
Since all vMAGs were identified by Virsorter2 and phamb, and have complete, high or medium quality evaluated by CheckV,
below is what I don't understand currently:
Thanks a lot!
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