stefanches7 / what_the_phage

Phage identification via nextflow/docker

What the Phage (WtP)

• by Christian Brandt & Mike Marquet
• this tool is currently under heavy development, so expect some bugs but feel free to report issues
• a save bet is to use release or pre release candidates via -r releasenumber e.g. -r v0.5
  • these are tested

What is this Repo?

• an attempt to streamline the usage of various phage identification and prediction tools
• the main focus is stability an data filtering / analysis for the user
• the tool is intended for fasta and nanopore fastq reads to identify phages in contigs/reads
• prophage detection is not implemented

The following Phage-Tools are currently included

• MARVEL Metagenomic Analysis and Retrieval of Viral Elements
  • paper
• VirFinder: R package for identifying viral sequences from metagenomic data using sequence signatures
  • paper
• PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
  • paper
• VirSorter
  • paper
• MetaPhinder
  • paper
• DeepVirFinder
  • paper
• Sourmash
  • paper
• VIBRANT
  • paper
• VirNet
  • paper

Workflow

Installation

• WtP runs with the workflow manager nextflow using docker
• this means all the other programs are automatically pulled via docker
• Only docker and nextflow needs to be installed

Easy Installation

• if you dont have experience with bioinformatic tools use this
• just copy the commands into your terminal to set everything up

sudo apt-get update
sudo apt install -y default-jre
curl -s https://get.nextflow.io | bash 
sudo mv nextflow /bin/
sudo apt-get install -y docker-ce docker-ce-cli containerd.io
sudo usermod -a -G docker $USER

• restart your computer

• try out the installation by entering the following

nextflow run replikation/What_the_Phage -r v0.5 --fasta ~/.nextflow/assets/replikation/What_the_Phage/test-data/all_pos_phage.fasta

Normal Installation

• this is the default choice

Dependencies

• docker (add docker to your Usergroup, so no sudo is needed)
• nextflow + java runtime
• git (should be already installed)
• wget (should be already installed)
• tar (should be already installed)

• Docker installation here
• Nextflow installation here
• move or add the nextflow executable to a bin path
• add docker to your User group via sudo usermod -a -G docker $USER

Execution

• for local use of the master branch you could either clone the git and do:

./phage.nf --fasta 'test-data/*.fasta'

• or execute it directly via a release candidate ( -r releasenumber , e.g. -r v0.5)

nextflow run replikation/What_the_Phage -r v0.5 --fasta 'your-fasta-files/*.fa'
# or
nextflow run replikation/What_the_Phage -r v0.5 --fasta your-file.fasta

• long-read input is supported via --fastq

Tool control

• all the tools can be separatly turned off via adding the related option flag
  • e.g. adding --ma to your command deactivates marvel
• execute --help for all options

# in this case Marvel (ma) and deepvirfinder (dv) are deactivated
nextflow run replikation/What_the_Phage -r v0.5 --fasta your-file.fasta --dv --ma

Temporary files

• all temporary files are stored in /tmp/nextflow-phage-$USER
• you can change the location via adding '-work-dir new/path/here' to the command

Results

• example output:

Help

nextflow run replikation/What_the_Phage --help
# or
./phage.nf --help