mir-seek

An awesome microRNA-sequencing pipeline

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

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 10 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary

Keywords

mature-mirna micro-rna micro-rna-expression mirdeep2 mirna mirna-seq singularity snakemake

Last synced: 6 months ago · JSON representation ·

Repository

An awesome microRNA-sequencing pipeline

Basic Info

Host: GitHub
Owner: OpenOmics
License: mit
Language: Python
Default Branch: main
Homepage: https://openomics.github.io/mir-seek/
Size: 595 KB

Statistics

Stars: 2
Watchers: 1
Forks: 1
Open Issues: 2
Releases: 2

Topics

mature-mirna micro-rna micro-rna-expression mirdeep2 mirna mirna-seq singularity snakemake

Created almost 3 years ago · Last pushed 11 months ago

Metadata Files

Readme Changelog License Citation

mir-seek 🔬

**_An awesome microRNA-sequencing pipeline_** [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13834237.svg)](https://doi.org/10.5281/zenodo.13834237) [![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/OpenOmics/mir-seek?color=blue&include_prereleases)](https://github.com/OpenOmics/mir-seek/releases) [![Docker Pulls](https://img.shields.io/docker/pulls/skchronicles/mir-seek)](https://hub.docker.com/repository/docker/skchronicles/mir-seek)
[![tests](https://github.com/OpenOmics/mir-seek/workflows/tests/badge.svg)](https://github.com/OpenOmics/mir-seek/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/mir-seek/workflows/docs/badge.svg)](https://github.com/OpenOmics/mir-seek/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/mir-seek?color=brightgreen)](https://github.com/OpenOmics/mir-seek/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/mir-seek)](https://github.com/OpenOmics/mir-seek/blob/main/LICENSE) This is the home of the pipeline, mir-seek. Its long-term goals: to accurately estimate microRNA expression, to perform quality-control, and to boldly discover known and novel miRNAs like no pipeline before!

Overview

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

The ./mir-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:

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

mir-seek is a comprehensive microRNA-sequencing pipeline. 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 single-end 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: singularity>=3.5 snakemake>=6.0 snakemake<8.0

At the current moment, the pipeline uses a mixture of enviroment modules and docker images; however, this will be changing soon! In the very near future, the pipeline will only use docker images. 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 will rely on versioned images from DockerHub. Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity will be the only two dependencies in the future.

Installation

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

Clone Repository from Github

git clone https://github.com/OpenOmics/mir-seek.git

Change your working directory

cd mir-seek/

Add dependencies to $PATH

Biowulf users should run

module load snakemake singularity

Get usage information

./mir-seek -h ```

Contribute

This site is a living document, created for and by members like you. mir-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

Please note that more citation formats and releases can be found on the mir-seek zenodo page.

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

@BibText

```text @software{Kuhn_OpenOmics_mir-seek_2024, author = {Skyler, Kuhn and Gary, Zhang}, title = {OpenOmics/mir-seek: v0.3.0}, month = sep, year = 2024, publisher = {Zenodo}, version = {v0.3.0}, doi = {10.5281/zenodo.13834238}, url = {https://doi.org/10.5281/zenodo.13834238} } ```

@APA

```text Skyler, K., & Gary, Z. (2024). OpenOmics/mir-seek: v0.3.0 (v0.3.0). Zenodo. https://doi.org/10.5281/zenodo.13834238 ```

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

Repositories: 9
Profile: https://github.com/OpenOmics

Open Bioinformatics Research

Citation (CITATION.cff)

authors:
- affiliation: National Institute of Allergy and Infectious Diseases
  family-names: Skyler
  given-names: Kuhn
  orcid: 0000-0003-0606-2125
- affiliation: National Institute of Allergy and Infectious Diseases
  family-names: Gary
  given-names: Zhang
  orcid: 0000-0002-3313-6030
cff-version: 1.2.0
message: "If you use mir-seek, please cite it as below."
date-released: '2024-09-24'
doi: 10.5281/zenodo.13834237
license:
- cc-by-4.0
repository-code: https://github.com/OpenOmics/mir-seek/
title: 'OpenOmics/mir-seek'
type: software

GitHub Events

Total

Watch event: 1
Issue comment event: 4
Push event: 4
Create event: 1

Last Year

Watch event: 1
Issue comment event: 4
Push event: 4
Create event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 58
Total Committers: 1
Avg Commits per committer: 58.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 58
Committers: 1
Avg Commits per committer: 58.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
skchronicles	k**3@g**m	58

Issues and Pull Requests

Last synced: about 2 years ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

skchronicles (2)

Pull Request Authors

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

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/mir-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

mir-seek

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

mir-seek 🔬

Overview

Dependencies

Installation

Clone Repository from Github

Change your working directory

Add dependencies to $PATH

Biowulf users should run

Get usage information

Contribute

Cite

References

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies