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mpox-seek

A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing

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

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 11 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary

Keywords

conda mamba monkeypox mpox oxford-nanopore phylogenetics pipeline rapid singularity snakemake
Last synced: 6 months ago · JSON representation ·

Repository

A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
conda mamba monkeypox mpox oxford-nanopore phylogenetics pipeline rapid singularity snakemake
Created almost 2 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License Citation

README.md

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.

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 is a streamlined viral metagenomics pipeline to align, collapse, and visualize targeted or whole-genome 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: ```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.

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 ```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 in addition to the zenodo DOI above. For more zenodo citation style options, please visit the pipeline's Zenodo page.

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.

Owner

  • Name: OpenOmics
  • Login: OpenOmics
  • Kind: organization
  • Location: United States of America

Open Bioinformatics Research

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- affiliation: National Institute of Allergy and Infectious Diseases
  family-names: Kuhn
  given-names: Skyler
  orcid: 0000-0003-0606-2125
- affiliation: National Institute of Allergy and Infectious Diseases
  family-names: Schaughency
  given-names: Paul
  orcid: 0000-0002-3358-2102
title: 'OpenOmics/mpox-seek'
date-released: '2024-04-10'
doi: 10.5281/zenodo.10957607
repository-code: https://github.com/OpenOmics/mpox-seek/
type: software

GitHub Events

Total
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 14
Last Year
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 14

Dependencies

.github/workflows/docs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/main.yaml actions
  • actions/checkout v2 composite
  • docker://snakemake/snakemake v5.24.2 composite
docker/mpox-seek/Dockerfile docker
  • ubuntu 22.04 build
docs/requirements.txt pypi
  • GitPython ==3.1.7
  • Jinja2 ==2.11.3
  • Markdown ==3.2.2
  • MarkupSafe ==1.1.1
  • PyYAML >=5.4
  • babel >=2.9.1
  • click ==7.1.2
  • future ==0.18.2
  • gitdb ==4.0.5
  • htmlmin ==0.1.12
  • importlib-metadata >=3.10
  • joblib ==0.16.0
  • jsmin ==3.0.0
  • livereload ==2.6.1
  • lunr ==0.5.8
  • mike *
  • mkdocs >=1.3.0
  • mkdocs-awesome-pages-plugin ==2.2.1
  • mkdocs-git-revision-date-localized-plugin ==0.7
  • mkdocs-git-revision-date-plugin *
  • mkdocs-material *
  • mkdocs-material-extensions *
  • mkdocs-minify-plugin ==0.3.0
  • mkdocs-redirects ==1.0.1
  • nltk >=3.6.6
  • pygments >=2.12
  • pymdown-extensions *
  • pytz ==2020.1
  • regex *
  • six ==1.15.0
  • smmap ==3.0.4
  • tornado ==6.0.4
  • tqdm ==4.48.2
  • zipp ==3.1.0