https://github.com/openomics/mpox-seek

A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
https://github.com/openomics/mpox-seek

conda mamba monkeypox mpox oxford-nanopore phylogenetics pipeline rapid singularity snakemake

Last synced: 4 months ago
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A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing

• Host: GitHub
• URL: https://github.com/openomics/mpox-seek
• Owner: OpenOmics
• License: mit
• Created: 2024-03-29T15:01:14.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2025-05-20T13:54:36.000Z (about 1 year ago)
• Last Synced: 2025-09-05T07:43:38.085Z (9 months ago)
• Topics: conda, mamba, monkeypox, mpox, oxford-nanopore, phylogenetics, pipeline, rapid, singularity, snakemake
• Language: Python
• Homepage: https://openomics.github.io/mpox-seek
• Size: 712 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

          


   

  
mpox-seek 🔬

  

  **_An ONT Pipeline for targeted or whole-genome Monkeypox sequencing_**


  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10957607.svg)](https://doi.org/10.5281/zenodo.10957607) [![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/OpenOmics/mpox-seek?color=blue&include_prereleases)](https://github.com/OpenOmics/mpox-seek/releases) [![Docker Pulls](https://img.shields.io/docker/pulls/skchronicles/mpox-seek)](https://hub.docker.com/repository/docker/skchronicles/mpox-seek)
 [![tests](https://github.com/OpenOmics/mpox-seek/workflows/tests/badge.svg)](https://github.com/OpenOmics/mpox-seek/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/mpox-seek/workflows/docs/badge.svg)](https://github.com/OpenOmics/mpox-seek/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/mpox-seek?color=brightgreen)](https://github.com/OpenOmics/mpox-seek/issues)  [![GitHub license](https://img.shields.io/github/license/OpenOmics/mpox-seek)](https://github.com/OpenOmics/mpox-seek/blob/main/LICENSE) 

  

  

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

  



## Overview

Welcome to mpox-seek! Before getting started, we highly recommend reading through [mpox-seek's documentation](https://openomics.github.io/mpox-seek/).

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](https://openomics.github.io/mpox-seek/usage/run/): Run the mpox-seek pipeline with your input files.

 * [mpox-seek unlock](https://openomics.github.io/mpox-seek/usage/unlock/): Unlocks a previous runs output directory.

 * [mpox-seek install](https://openomics.github.io/mpox-seek/usage/install/): Download reference files locally.

 * [mpox-seek cache](https://openomics.github.io/mpox-seek/usage/cache/): Cache software containers locally.

**mpox-seek** is a streamlined viral metagenomics pipeline to align, collapse, and visualize targeted or whole-genome monekypox samples. It relies on technologies like [Singularity1](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake2](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from [Nanopore sequencing technologies](https://nanoporetech.com/). 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](https://openomics.github.io/mpox-seek/usage/run/) section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/mpox-seek/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/mpox-seek/issues).

## Dependencies

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

[Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) 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](https://singularity.lbl.gov/all-releases) OR [conda/mamba](https://github.com/conda-forge/miniforge#mambaforge), 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](https://openomics.github.io/mpox-seek/usage/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)](https://learn.microsoft.com/en-us/windows/wsl/install). Singularity can be installed on WSL following these [instructions](https://www.blopig.com/blog/2021/09/using-singularity-on-windows-with-wsl2/).

## Installation

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

```bash

# 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](https://openomics.github.io/mpox-seek/setup/).

## 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](https://github.com/OpenOmics/mpox-seek).

## Cite

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

  @BibText

 

```text

@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

```text

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

```

Please do not forget to also cite our [methods paper](https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2494733) in addition to the zenodo DOI above. For more zenodo citation style options, please visit the pipeline's [Zenodo page](https://doi.org/10.5281/zenodo.10957607).

## References

**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.