vClassifier v1.0

Introduction

Leveraging reference trees and nucleotide identity metrics, we developed the vClassifier toolkit. This tool streamlines and standardizes the taxonomic categorization of prokaryotic viral genomes. Benchmark comparisons revealed that vClassifier matches or surpasses other available tools in terms of precision and classification success rates. Accurate assignments at the subfamily, genus, and species levels will significantly enhance taxonomic resolution.

Please note that this is an ALPHA version of the program, which means this collection of scripts possiblely contains bugs and is still under development.

Preinstallation

Install a latest version of Miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-py312_24.7.1-0-Linux-x86_64.sh
bash Miniconda3-py312_24.7.1-0-Linux-x86_64.sh
conda activate

How to install vClassifier

1. copy to your profile the content of the vClassifier folder

git clone https://github.com/AnantharamanLab/vClassifier.git
cd vClassifier/database
unzip packages_for_pplacer.zip
unzip VOG_protein_sequences_at_FamilyOrSubfamily_rank.zip
gzip -d reference_genomes.fasta.gz
wget https://fileshare.lisc.univie.ac.at/vog/vog216/vog.hmm.tar.gz
mkdir VOG_hmmfiles
cd VOG_hmmfiles && tar -zxf ../vog.hmm.tar.gz && cd -

2. add a directory to your $PATH

export PATH="/PATH/TO/vClassifier:$PATH"   #change /PATH/TO to the installation path of vClassifier

Please note that if you want to permanently set $PATH on Linux, add the above command to your ~/.profile or ~/.bashrc file and run:

source ~/.profile 
or
source ~/.bashrc

3. create and activate the vClassifier conda env

Create env via conda:

conda env create -f /Path/To/vClassifier.yml   #change /PATH/TO to the installation path of vClassifier 
conda activate vClassifier

Alternatively, create env via mamba to accelerate installation:

conda install mamba -c conda-forge
mamba env create -f /Path/To/vClassifier.yml   #change /PATH/TO to the installation path of vClassifier 
conda activate vClassifier

If you encounter the following errors during installation:

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 is excluded by strict repo priority
  - package perl-file-path-2.18-pl5321hd8ed1ab_0 is excluded by strict repo priority
  - package perl-file-temp-0.2304-pl5321hd8ed1ab_0 is excluded by strict repo priority
  - package perl-file-which-1.24-pl5321hd8ed1ab_0 is excluded by strict repo priority

​Please enter the following command to set the channel priority to flexible:

conda config --set channel_priority flexible

Afterward, rerun the command:

conda env create -f /Path/To/vClassifier.yml  #change /PATH/TO to the installation path of vClassifier
conda activate vClassifier

Or

mamba env create -f /Path/To/vClassifier.yml   #change /PATH/TO to the installation path of vClassifier 
conda activate vClassifier

Running vClassifier

Two main programs are implemented in vClassifier: vClassifier for viral families and for viral subfamilies. In summary, the first one is used to assign taxonomy to viral genomes of the 36 reference families that have been listed in the /database/reference_family_list, while the second is used to assign taxonomy to viruses of the 55 reference subfamilies that have been listed in the /database/reference_family_list.

Quick Start

Usage:

vClassifier -m "mode" -i "/PATH/TO/Input" -l "/PATH/TO/Taxa" -p "/Full/PATH/TO/Installation" -o "Output directory" -t "Number of threads"

Option descriptions:

-i Input nucleotide sequences in FASTA format. Please note that providing the full path is recommended to avoid errors.

-l A file containing family or subfamily information for the input nucleotide sequences. The first column should list the query IDs, and the second column should provide the corresponding family or subfamily taxonomy. Please note that providing the full path is recommended to avoid errors.

-t Number of threads to use for parallel running.

-p Full installation path for vClassifier. Please verify that the directories for the database and scripts are present under this path.

-m vClassifier mode. Input 'family' or 'subfamily' only. Mode 'family': inputs are viral genomes that include family information. Mode 'subfamily': inputs are viral genomes that include subfamily information.

-o Output directory.

-h Show help on version and usage.

Output descriptions:

• The final output file, "sequences_with_classification.txt", contains the taxonomic assignments for the query genomes.
• The intermediate output directory, gene_calling, contains files generated during gene prediction.
• The intermediate output directory, genome_alignment, contains files produced during the alignment of single-copy genes of queries with those of references.
• The intermediate output directory, tree_replacement_and_taxon_assignment, holds outputs generated during reference tree replacement and taxon assignment.

Testing vClassifier

vClassifier for viral families

Example:

vClassifier -m family -i "/PATH/TO/vClassifier/example_data/examples_of_viral_genomes_that_include_family_information/query_genomes.fna" -l "/PATH/TO/vClassifier/example_data/examples_of_viral_genomes_that_include_family_information/query_family" -p "/Full/PATH/TO/vClassifier" -o Output_dir -t 30

vClassifier for viral subfamilies

Example:

vClassifier -m subfamily -i "/PATH/TO/vClassifier/example_data/examples_of_viral_genomes_that_include_subfamily_information/query_genomes.fna" -l "/PATH/TO/vClassifier/example_data/examples_of_viral_genomes_that_include_subfamily_information/query_subfamily" -p "/Full/PATH/TO/vClassifier" -o Output_dir -t 30