Prophage Detection in Bacterial Genomes Have Different Result if I Use Different Program?

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Hasi Hays

Check for the particular pipeline's specific genomic annotations. Make sure the annotation version is the same. If it is you should find the same results.

I reckon that this might helpful.

Forbes Avila

Dear Dr. Hasi Hays

Thank you for the suggestions.

I use the most recent version of both programs.

However, Phaster.ca use alignment based and the PhiSpy use genes

So I just annotate and choose from both results based on blast and protein completeness?

Vikas Sharma

I used two different software (Virsorter2 & VIBRANT) and found differences in the number of identified prophages. However, comparing both results showed 70% accordance in terms of numbers with each other. Although I also identified position differences because identification of prophage boundaries is sometimes tricky. I think you observed differences because the tools you used uses different tools and databases. I hope this information will be helpful to you.

Dear Dr Vikas Sharma

Thank you for the information. May I ask you how do you interpret or choose the best data from the two program do you use?

We chose the best tool based on the previous findings. In our case, Virsorter2 was missing a lot of major prophages according to previous publications, on the other hand, VIBRANT detected most of the expected viral elements. Therefore, we decided to use VIBRANT for the final analysis. So, you must find the best publications to decide the best tool and validate your findings.

Thank you for the answers!