Installing and running Vcontact2

Overview

Teaching: 0 min
Exercises: 30 min

Questions

• How do we install and run Vcontact2?

Objectives

• Install & Run Vcontact2

Another way to visualise genome similarity based on gene sharing is by graphing them as networks. Vcontact2 is a popular tool perform taxonomic classification that uses gene sharing networks.

In short, Vcontact2 uses a two step clustering approach to first cluster proteins into protein clusters (PCs, similar to what you did in day 3) and then clusters genomes based on how many PCs they share. It then applies parameterised cut-offs to decide whether genomes are similar enough to be considered as belonging to the same genus. For more information please read the Vcontact2 paper or repository.

We will start vContact2 before lunch because it takes ~1 hour to run for our dataset. In the afternoon we will analyse the output.

0. Install Vcontact2

Installing vcontact2 is a bit of a mess due to some dependencies, so we will create a separate conda environment. Open a new terminal and do the following:

# create a new conda environment
$ conda create --name vContact2 python=3.7
$ conda activate vContact2

# pandas need to be 0.25.3
$ conda install pandas=0.25.3
$ conda install -c bioconda vcontact2
$ conda install -c bioconda -y mcl blast diamond

# Downgrade Numpy
$ conda install -c bioconda numpy=1.19.5

# Install ClusterONE
# Please remember where you put it, as you need to specify the path to cluster one when running vcontact2.
# cd /path/to/viromics/folder
wget --no-check-certificate https://paccanarolab.org/static_content/clusterone/cluster_one-1.0.jar

Next we are going to run vContact2. Vcontact2 comes with a test dataset to verify if it installed correctly, but because running this test takes ~1 hour we are going to skip it and directly test by analysing our own dataset.

Task 1: Create vContact2 input files

Read the Vcontact2 manual. What input do you need? Can you create these files?

solution

You need two files:

1. A FASTA-formatted amino acid file.
2. A “gene_to_genome” mapping file, in either tsv (tab)- or csv (comma)-separated format.

   echo "protein_id,contig_id,keywords" >> gene_to_genome.csv
   cat proteins_bins.faa | grep ">" | cut -f 1 -d " "  | sed 's/^>//g' > protein_ids.csv
   cat protein_ids.csv | sed 's/_[0-9]*$//g' >contig_ids.csv
   paste -d , protein_ids.csv contig_ids.csv >> gene_to_genome.csv 
   

Task 2: run Vcontact2

Check the Vcontact2 manual to find out how to do this.

solution

From within the vcontact environment, run:

vcontact2 --raw-proteins /path/to/proteinfile.faa --rel-mode 'Diamond' --proteins-fp /path/to/gene_to_genome.csv --db 'ProkaryoticViralRefSeq94-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /path/to/clusterone --output-dir /path/to/output/dir

Now that vContact2 is running enjoy your lunch break!

Key Points

• We’re running vContact2 over lunch because it takes around an hour to finish