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dyxstat / ViralCC

ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes
GNU Affero General Public License v3.0
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Retrieve virus-host pairs with ViralCC #6

Closed Kenkeni-ZJU closed 7 months ago

Kenkeni-ZJU commented 7 months ago

Hi Yuxuan,

I am trying to retrieve virus-host pairs with ViralCC since it seems that I can do this (according to your paper). However, there is no such information in the output files. Can I achieve this goal directly with ViralCC?

Thanks, Kankan

dyxstat commented 7 months ago

Hi Kankan,

The ViralCC software serves as a binning tool for viral contigs. To replicate the results regarding virus-host interactions presented in our paper, you'll then need to bin non-viral contigs using your preferred binning tools and generate the raw Hi-C contact matrix for all contigs including viral and non-viral contigs (tools like NormCC can facilitate this process).

Utilizing both the raw Hi-C contact matrix and the identified viral as well as non-viral bins, you can then discern the viral-host pairs.

Best

Kenkeni-ZJU commented 7 months ago

Thank you!