BKTyper is a human polyoma BK (BKPyV) typing tool. It can automatically classify transcriptional blocks from the Non-Coding Control Region (NCCR) and the Viral Protein 1 (VP1). It can take a nucleotide sequence in fasta format containing the complete BKPyV genome or subgenomic region containing the VP1 gene or the NCCR region.
BKTyper can be used online wihtout the need of further installation at https://bktyper.zidu.be/.
Please if you want to use either the online free tool or decide to use the local installation, please cite our work. This is an academical on-going work and it is meant to be mantained long-term. Citation will help ensuring that the server costs are mantained.
Citation: Martí-Carreras, J.; Mineeva-Sangwo, O.; Topalis, D.; Snoeck, R.; Andrei, G.; Maes, P. BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing. Viruses 2020, 12, 837.
BKTyper depends on 4 different external programs that should be installed in your operational system and be on path:
BKTyper is written in Python3 and depends on several Python libraries. Clone the repository and install the requiered Python libraries through CONDA for ease of installation:
git clone https://github.com/joanmarticarreras/BKTyper.git
cd BKTyper/
conda install -y --file requirements.txt
BKTyper requires a fasta file as input, which should contain a BKPyV nucleotide sequence (full genome, VP1 or NCCR regions). Additionally it requires as extra arguments the type of sequence is being input (complete for the complete genome, VP1 or NCCR as what the sequence contains). Finally, it is possible to have phylogenetic placing throuigh a Maxmimum-Likelihood tree with IQTree, type "Tree" or "noTree" as to enable the options (for "complete" or "VP1" mode only).
python3 BKTyper.py <input-sequences> <mode: VP1, NCCR, complete> <phylogeny: Tree noTree>