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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Prophage regions #86

Open niamhlacy opened 3 years ago

niamhlacy commented 3 years ago

Hello,

I was wondering how exactly VirSorter defines a prophage regions and if there is a way to get the coordinates of the prophage regions identified?

Thanks, Niamh

simroux commented 3 years ago

Hi,

VirSorter is using a sliding window approach to find "viral-like regions" within input contigs. When the "best" viral-like region covers less than 80% of the contig, VirSorter then considers that the contig includes both a viral and a host region (i.e. includes an integrated prophage). You can find more details in the original VirSorter publication: https://peerj.com/articles/985/

Depending your version of VirSorter, you can get the coordinates of the prophage regions identified in the file "_global-phage-signal-.csv", or you can get the gene identifiers corresponding to the boundaries of the prophage from the file "_global-phage-signal.csv" and then identify the corresponding coordinates in the file "_affi-contigs.csv".

Best, Simon