openomics/mpox-seek

A rapid pipeline for targeted ONT monkeypox sequencing

mpox-seek 🔬

Targeted ONT Pipeline for Monkeypox

mpox-seek is an awesome, portable and fast oxford nanopore pipeline for targeted monkeypox sequencing.

Overview

Welcome to mpox-seek! Before getting started, we highly recommend reading through mpox-seek's documentation.

The ./mpox-seek pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

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

mpox-seek is a streamlined viral metagenomics pipeline to align, collapse, and visualize targeted monekypox 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 Nanopore 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 trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.

Dependencies

Requires: snakemake<8.0 conda/mamba singularity>=3.5 (optional)

Snakemake must be installed on the target system. Snakemake is a workflow manager that orchestrates each step of the pipeline. The second dependency, i.e singularity OR conda/mamba, handles the dowloading/installation of any remaining software dependencies. By default, the pipeline will utilize singularity to guarantee the highest level of reproducibility; however, the --use-conda option of the run sub command can be provided to use conda/mamba instead of singularity. If possible, we recommend using singularity over conda for reproducibility; however, it is worth noting that singularity and conda produce identical results for this pipeline. If you plan on running this pipeline on a laptop or desktop computer, we recommend using conda/mamba over singularity.

If you are running the pipeline on Windows, please use the Windows Subsystem for Linux (WSL). Singularity can be installed on WSL following these instructions.

Installation

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

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

For more detailed installation instructions, please see our setup page.

Contribute

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

Cite

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

@BibText

@software{Kuhn_OpenOmics_mpox-seek_2024,
  author       = {Skyler Kuhn and Schaughency, Paul},
  title        = {OpenOmics/mpox-seek: v0.1.0},
  month        = apr,
  year         = 2024,
  publisher    = {Zenodo},
  version      = {v0.1.0},
  doi          = {10.5281/zenodo.10957607},
  url          = {https://doi.org/10.5281/zenodo.10957607}
}

@APA

Skyler Kuhn, & Schaughency, P. (2024). OpenOmics/mpox-seek: v0.1.0 (v0.1.0). Zenodo. https://doi.org/10.5281/zenodo.10957607

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>