Setup and run VirSorter

Overview

Teaching: 10 min
Exercises: 20 min

Questions

• How do we install and run VirSorter?

• How is VirSorter different than the previous tools?

Objectives

• Install and run VirSorter

The last virus identification tool, which we will run over lunch, is called VirSorter (Roux et al. 2015). VirSorter is different from the other tools in that it actually considers homology in predicting whether a contig belongs to a phage or a microbe. VirSorter distinguishes between “primary” and “secondary” metrics when deciding how to annotate a sequence. Primary metrics are the presence of viral hallmark genes an their homologs, and the enrichment of known viral genes. Secondary metrics include an enrichment in uncharacterized genes, depletion of PFAM-affiliated genes, and two metrics of genome structure.

Challenge: Viral genome structure

VirSorter uses two genome structure metrics to distinguish phage sequences from bacterial sequences. Can you think of viral genome structure metrics that could be useful for prediction?

Solution

VirFinder uses:

1. an enrichment of short genes
2. depletion in strand switch

To run VirSorter, first create the necessary environment from virsorter.yaml and activate it. Then, download virsorter into the day2/tools folder. Note that the following code is in bash again.

# Install Virsorter
$ cd ~/ViromicsCourse/day2/tools
$ git clone https://github.com/simroux/VirSorter.git
$ cd VirSorter/Scripts
$ make clean
$ make

# Make symbolic link of executable scripts in the environment's bin
# It is important to use the absolute path and not the relative path to the Scripts folder (replace XXX with the number of your account, or replace the absolute path with the path to your own anaconda if you join online)
$ ln -s ~/ViromicsCourse/day2/tools/VirSorter/wrapper_phage_contigs_sorter_iPlant.pl /mnt/local/prakXXX/anaconda3/envs/virsorter/bin
$ ln -s ~/ViromicsCourse/day2/tools/VirSorter/Scripts /mnt/local/prakXXX/anaconda3/envs/virsorter/bin

Finally, install metagene_annotator into the conda environment.

# Install metagene_annotator
$ conda install metagene_annotator -c bioconda

Finally, run VirSorter. Note that VirSorter is very particular about its working directory. It is best if it doesn’t exist beforehand (VirSorter will create it). If a run fails, then completely remove the working directory before you restart it.

# Run VirSorter
# Under the argument --data-dir put the link https://blahblah.com/virsorter-data
$ wrapper_phage_contigs_sorter_iPlant.pl -f ~/ViromicsCourse/day2/scaffolds_over_300.fasta --db 1 --wdir ~/ViromicsCourse/day2/results/virsorter --ncpu 1 --data-dir ~/ViromicsCourse/day2/tools/virsorter-data

If your run fails because “Step 1 failed”, then check the error file in ~/ViromicsCourse/day2/results/virsorter/logs/. If the error is “Can’t locate Bio/Seq.pm in @inc (you may need to install the Bio::Seq module)…”, then you need to copy a perl folder in the virsorter environment folder.

# Error fix for Can't locate Bio/Seq.pm in @inc
$ cd /mnt/local/prakXXX/anaconda3/envs/virsorter/lib/
$ cp -r perl5/site_perl/5.22.0/Bio/ site_perl/5.26.2/x86_64-linux-thread-multi/

Then try to run the command again. If you have more problems, let us know. Guten Appetit! Eet smakkelijk! Have a good lunch!

Key Points

• VirSorter is a homology-based tool.

• Because Virsorter has to compare each sequence to a database, it is slower that many other tools.