Overview

What is it

A reads to report workflow for metavirome analysis:

• Raw reads cleanup and profiling with Kraken2
• Assembly with Megahit (overview with MetaQuast)
• Phage mining with:
  • VirFinder
  • VirSorter
  • Phigaro
  • Vibrant
• Consensus (cd-hit) and backmapping (bowtie2), and quantification (bamtocov)
• Genefinding and viral taxonomy (vContact2)
• Comprehensive report

Workflow manager

The workflow is written in Nextflow, a DSL and task orchestrator that allows the reproducible execution and scale up from:

• local execution (e.g. virtual machine)
• HPC (Slurm, PBS…)
• Cloud (Amazon, Google,…)

The dependencies can be easily installed, via:

• Docker
• Singularity
• Conda environment

To get started

A complex pipeline requires a lot of dependencies and the appropriate resources to parallelize the execution of concurrent tasks.

Nextflow allows the user to have a custom configuration specifying how to execute the tasks (locally, in a cluster, on the cloud) and where to find the packages (Singularity, Docker).

Finally, MetaPhage needs a set of databases that can be easily downloaded with a script provided in the repository.

The workflow