ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

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Introduction

ViroProfiler is a bioinformatics best-practice analysis pipeline for viral metagenomics data analyses.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.

Quick Start

1. Install one of the supported container engines using root privileges:

   • Singularity
   • Charliecloud
   • Docker
   • Podman
   • Shifter

2. Install Miniconda3.

3. Install Nextflow using conda:

   # You may need to restart your terminal before running the following commands
   conda install -c bioconda nextflow

4. Download the pipeline and database.

   # setup database
   nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup"

   -profile specifies the container engine to use. You can use singularity, charliecloud, docker, podman, or shifter. You can also use test to run the pipeline with test data after setting up the database.

5. Run the pipeline,

   # run test
   nextflow run deng-lab/viroprofiler -r main -profile singularity,test
   
   # run your own data
   nextflow run deng-lab/viroprofiler -r main -profile singularity --input samplesheet.csv

6. Update the pipeline,

   nextflow pull deng-lab/viroprofiler

   Please refer to the tutorial for more information on how to run the pipeline with customized parameters and options.

Documentation

Please refer to the documentation.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, please open an issue.

Citations

If you use ViroProfiler for your analysis, please cite the publication as follows:

Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng. ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis. Gut Microbes (2023); doi: https://doi.org/10.1080/19490976.2023.2192522

An extensive list of references for the tools and data used by the pipeline can be found in the CITATIONS.md file. If you use ViroProfiler for your work, please cite the relevant references.