Annotation-only wrapper for VIBRANT
Kristopher Kieft
January 2022
The purpose of this tool is to skip the virus prediction methods of VIBRANT and only annotate the input sequences with the exact same method used by VIBRANT. It is compatible with VIBRANT v1.2.1.
IMPORTANT: This is an extension of the main package VIBRANT. You must have the VIBRANT databases and associated files downloaded and available.
Run these two export commands or put them in your .bashrc/.bash_profile. Replace full_path_here with your actual path. Alternatively, you can skip this and specify these two folders with -d and -m, respectively.
export VIBRANTAUX='full_path_here/VIBRANT_v1.2.1/files/'
export VIBRANTDB='full_path_here/VIBRANT_v1.2.1/databases/'
annoVIBRANT.py -i example_seqs.fna -t 2 -o annoVIBRANT_output_folder
Note: you can run proteins as well, input them with -i and specify -f prot. If you use proteins they just have to be in Prodigal format ("name_of_scaffold_#").