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
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
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de
Developer - Cristina Moraru, PhD
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de
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.)
Developer - Cristina Moraru, PhD
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de