README.md

metavirs 🔬

Viral Metagenomics Pipeline

This is the home of the pipeline, metavirs. Its long-term goals: are to assemble, annotate, and screen environmental samples like no pipeline before!

Overview

Welcome to metavirs! Before getting started, we highly recommend reading through metavirs' documentation.

The ./metavirs pipeline is composed of several inter-related subcommands to set up and run the pipeline across different systems. Each of the available sub-commands performs different functions:

• metavirs run: Run the metavirs pipeline with your input files.
• metavirs unlock: Unlocks a previous runs output directory.
• metavirs install: Download reference files locally.
• metavirs cache: Cache software containers locally.

metavirs is a comprehensive viral metagenomics pipeline to assemble, annotate, and classify microorganisms in environmental samples. It relies on technologies like Singularity¹ to maintain the highest level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake², a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub-command.

For more information about issues or troubleshooting a problem, please check out our FAQ prior to opening an issue on Github.

Dependencies

Requires: singularity>=3.5 snakemake>=6.0

At the current moment, the pipeline only has two dependencies: snakemake and singularity. With that being said, snakemake and singularity must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step of the pipeline relies on versioned images from DockerHub.

Installation

Please clone this repository to your local filesystem using the following command:

# Clone Repository from Github
git clone https://github.com/OpenOmics/metavirs.git
# Change your working directory
cd metavirs/
# Add dependencies to $PATH
# Biowulf users should run
module load snakemake singularity
# Get usage information
./metavirs -h

Contribute

This site is a living document, created for and by members like you. metavirs is maintained by the members of OpenOmics and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull requests to our GitHub repository.

Citation

If you use this software, please cite it as below:

@BibTex

@software{Kuhn_OpenOmics_metavirs_2022,
    author = {Kuhn, Skyler and Schaughency, Paul},
    doi = {10.5281/zenodo.7120936},
    month = {9},
    title = {{OpenOmics/metavirs}},
    url = {https://github.com/OpenOmics/metavirs/},
    year = {2022}
}

@APA

Kuhn, S., & Schaughency, P. (2022). OpenOmics/metavirs [Computer software]. https://doi.org/10.5281/zenodo.7120936

For more citation style options, please visit the pipeline's Zenodo page.

References

<sup>1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>