replikation/r-phage-plot repository overview

⁠What the Phage (WtP)

• by Christian Brandt & Mike Marquet

⁠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 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

⁠Installation

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

⁠Dependencies

⁠Execution

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

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

• or execute it directly via

nextflow run replikation/wf_phage_benchmark --fasta 'your-fasta-files/*.fasta'
# or
nextflow run replikation/wf_phage_benchmark --fasta your-file.fasta

⁠Help

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