Andrea Telatin
Andrea Telatin Senior bioinformatician at the Quadram Institute Bioscience, Norwich.

EBAME-7 Viromics notes

EBAME-7 Viromics notes

This “virome primer” is designed to provide a short overview on viromics and the tools available to analyse viral metagenomes. The tutorial is agnostic to the environment, and can be followed on any linux system. This page has some notes specific for the Virtual Machines used during the EBAME-7 Workshop.

:warning: This whole website is a reference, not a step-by-step guide. attempting to copy and paste commands can lead to errors or very long computation times. Let’s chat on Slack!

Initialize conda, instal mamba

You already have conda Installed, let’s install mamba too (a faster drop-in replacement):



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conda init bash
conda install -c conda-forge --yes mamba

Screen

If you plan to use GNU Screen, you can download a configuration file to show a status bar:



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wget -O "$HOME/.screenrc" "https://gist.githubusercontent.com/telatin/66fab72e9bf0dda9984cad8d97c6174b/raw/381014e047cd0d04990176b83e0b723363dda93d/.screenrc"

Databases and datasets location

We have a dedicated partition for databases and datasets, which we can link to a $VIR variable for easier access.

:information_source: Copy and paste the following commands to setup your VM for the Viromic tutorial!



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# To make it permanent
mkdir -p $HOME/bin/
echo 'export VIR=/ifb/data/public/teachdata/ebame-2022/virome/' >> ~/.bashrc
echo 'export PATH=$PATH:$HOME/bin:/ifb/data/public/teachdata/ebame-2022/virome/bin/' >> ~/.bashrc
echo 'export PHANTA_DIR=/ifb/data/public/teachdata/ebame-2022/virome/phanta/' >> ~/.bashrc
echo 'export PHANTA_DB=/ifb/data/public/teachdata/ebame-2022/virome/phanta_dbs/default_V1/' >> ~/.bashrc
echo 'shopt -s direxpand' >> ~/.bashrc

# Load the settings
source ~/.bashrc

To check that the variable is set correctly, you can run:



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ls $VIR/

it should list (more or less) the following files:



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drwxrwxr-x 2 ubuntu ubuntu         530 Oct 25 14:56 bin
drwxrwxr-x 2 ubuntu ubuntu         492 Oct 20 14:36 dataset
drwxrwxr-x 2 ubuntu ubuntu         843 Oct 20 14:38 dataset-full
drwxrwxr-x 6 ubuntu ubuntu         292 Oct 25 14:56 phanta
drwxrwxr-x 4 ubuntu ubuntu         110 Oct 21 08:55 phanta-out
drwxrwxr-x 3 ubuntu ubuntu          28 Oct 20 10:35 phanta_dbs
drwxrwx--- 2 ubuntu ubuntu         152 Aug  2 21:52 test_dataset
drwxrwxr-x 7 ubuntu ubuntu         398 Oct 20 14:19 vcontact2
-rw-rw-r-- 1 ubuntu ubuntu        4110 Oct 20 11:04 vcontact2.yaml
drwxrwxr-x 7 ubuntu ubuntu         153 Oct 19 14:41 virsorter2

What do we have?

  • Datasets, both the full dataset and a very reduced one are available at $VIR/dataset-full and $VIR/dataset, respectively.
  • Phanta, the virome aware profiler, is available at $VIR/phanta
    • Phanta Database is available at $VIR/phanta_dbs/default_V1
  • VirSorter 2 is downloaded to $VIR/virsorter2
  • vConTACT2 is downloaded to $VIR/vcontact2 and its environment is available at $VIR/vcontact2.yaml

Datasets

:bulb: Need a single sample to test your commands with? Use $VIR/dataset/SRR8652861_1.fq.gz.

  • A reduced dataset with a few reads is available at $VIR/dataset (45 Mb total). In the interest of time, we will use this one during the workshop.
    • SRR8652861
    • SRR8652914
    • SRR8652969
    • SRR8653218
    • SRR8653221
    • SRR8653245
  • The raw reads are available at $VIR/dataset-full (6.8G total). This is still reasonably sized and can be used at your pace in the VM.

Create environments

:one: We will use conda to create environments for the different tools.



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mamba env create -n phanta --file ${VIR}/phanta/phanta_env.yaml

:two: Install VirSorter2 in a dedicated environment



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mamba create -n vs2  --yes -c conda-forge -c bioconda \
    "python>=3.6" scikit-learn=0.22.1 \
    imbalanced-learn pandas seaborn hmmer==3.3 prodigal \
    screed ruamel.yaml "snakemake>=5.18,<=5.26" \
    click mamba virsorter=2

:three: Optionally, you can create an environment to run vConTACT2:



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mamba env create -n vcontact2 --file ${VIR}/vcontact2.yaml

##

The programme

  • :zero: EBAME-22 notes: EBAME-7 specific notes
  • :one: Gathering the reads: downloading and subsampling reads from public repositories (optional)
  • :two: Gathering the tools: we will use Miniconda to manage our dependencies
  • :three: Reads by reads profiling: using Phanta to quickly profile the bacterial and viral components of a microbial community
  • :four: De novo mining: assembly based approach, using VirSorter as an example miner
  • :five: Viral taxonomy: ab initio taxonomy profiling using vConTACT2
  • :six: MetaPhage overview: what is MetaPhage, a reads to report pipeline for viral metagenomics

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