Whats is VIRIDIC and how to cite
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. The algorithms used are presented in the paper:
Moraru, C., Varsani, A., and Kropinski, A.M. (2020) VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11). https://doi.org/10.3390/v12111268
Important notes:
1. To run VIRIDIC web, upload a single fasta file with all phage genomes of interest, create a project and press run. Save the project ID that will be displayed when the project is created. You will need it to access the data if the calculations take a long time.
2. In the input fasta file, the identifier of each fasta record should be unique and it should have no spaces. Spaces can be replaced with '_'.
3. VIRIDIC stand-alone is available now (see download tab). You can use it for jobs with high computational demand and/or for implementing it in your own pipelines. It is very easy to install on your own servers (it is wrapped as a Singularity). You can continue to use the VIRIDIC web-service for small to medium projects (e.g. up to 200 phages per project, no viromes please, they will crash our resources and the analysis will fail).
News
You can download the VIRIDIC source code (stand-alone and shiny app), including the YAML file for the corresponding conda environment from the GitHub Repo: VIRIDIC repo
VirClust, a tool for hierarchical clustering of viruses, core protein calculation and protein annotation, is now available at virclust.icbm.de .
Developer - Cristina Moraru, PhD
I've developed VIRIDIC during my possition as Senior Scientist in the Department of The Biology of Geological Processes, at the Institute for Chemistry and Biology of the Marine Environment, Germany. The VIRIDIC web-site and web-service are hosted at this institution.
My current possition is that of Senior Scientist in the Environmental Metagenomics Department, at the Research Center One Health Ruhr of the University Alliance Ruhr, Essen, Germany.
Please post any VIRIDIC related problems or feature requests here in the Issues section of the correponding github repository.
Developer - Cristina Moraru, PhD
I've developed VIRIDIC during my possition as Senior Scientist in the Department of The Biology of Geological Processes, at the Institute for Chemistry and Biology of the Marine Environment, Germany. The VIRIDIC web-site and web-service are hosted at this institution.
My current possition is that of Senior Scientist in the Environmental Metagenomics Department, at the Research Center One Health Ruhr of the University Alliance Ruhr, Essen, Germany.
Please post any VIRIDIC related problems or feature requests here in the Issues section of the correponding github repository.
Algorithms used by VIRIDIC and how to cite
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. The algorithms used are presented in the paper “VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses”, co-authored by Cristina Moraru, Arvind Varsani and Andrew Kropinski. You can access this paper here: doi: 10.3390/v12111268
NEW: Download VIRIDIC v1.1 stand-alone
VIRIDIC v1.1 has a new parameter, named ram_max. This allows the user to set the maximum amount of RAM used (controls basically the future_globals_max_size_default option in R.)
Download VIRIDIC source code
You can download the VIRIDIC source code (stand-alone and shiny app), including the YAML file for the corresponding conda environment from the GitHub Repo: VIRIDIC repo
Developer - Cristina Moraru, PhD
I've developed VIRIDIC during my possition as Senior Scientist in the Department of The Biology of Geological Processes, at the Institute for Chemistry and Biology of the Marine Environment, Germany. The VIRIDIC web-site and web-service are hosted at this institution.
My current possition is that of Senior Scientist in the Environmental Metagenomics Department, at the Research Center One Health Ruhr of the University Alliance Ruhr, Essen, Germany.
Please post any VIRIDIC related problems or feature requests here in the Issues section of the correponding github repository.