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 Miniconda3.

2. Install Nextflow and Singularity using conda:

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

3. Download the pipeline and database.

   nextflow run deng-lab/viroprofiler -profile singularity

4. Run the pipeline,

   nextflow run deng-lab/viroprofiler -profile singularity --input samplesheet.csv

   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

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.