https://github.com/vanheeringen-lab/seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
https://github.com/vanheeringen-lab/seq2science

atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows

Last synced: 4 months ago
JSON representation

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

• Host: GitHub
• URL: https://github.com/vanheeringen-lab/seq2science
• Owner: vanheeringen-lab
• License: mit
• Created: 2019-07-11T11:12:45.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-02-05T14:07:13.000Z (about 1 year ago)
• Last Synced: 2024-05-22T16:36:13.180Z (11 months ago)
• Topics: atac-seq, bioinformatics, bioinformatics-pipeline, chip-seq, fastq, ngs, pipeline, reproducible-research, rna-seq, snakemake, sra, workflows
• Language: Python
• Homepage: https://vanheeringen-lab.github.io/seq2science
• Size: 1.39 GB
• Stars: 146
• Watchers: 6
• Forks: 26
• Open Issues: 24
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: docs/CONTRIBUTING.md
  • License: LICENSE
  • Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

• awesome-atac-analysis - seq2science

README

        
# seq2science

[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/seq2science/README.html)

[![anaconda-version](https://anaconda.org/bioconda/seq2science/badges/version.svg)](https://anaconda.org/bioconda/seq2science/badges/version.svg)

[![nr downloads](https://img.shields.io/conda/dn/bioconda/seq2science.svg?style=flat)](http://bioconda.github.io/recipes/seq2science/README.html)

[![star this repo](https://img.shields.io/github/stars/vanheeringen-lab/seq2science?style=flat&color=brightgreen)](https://github.com/vanheeringen-lab/seq2science/stargazers)

[![Test Status](http://ocimum.science.ru.nl/jenkins/buildStatus/icon?job=seq2science%2Fmaster&subject=tests)](http://ocimum.science.ru.nl/jenkins/job/seq2science/job/master/lastBuild/display/redirect/)

[![docs](https://github.com/vanheeringen-lab/seq2science/workflows/docs/badge.svg)](https://vanheeringen-lab.github.io/seq2science)

[![DOI](https://img.shields.io/badge/DOI-10.7717%2Fpeerj.16380-%2302A7FC)](https://doi.org/10.7717/peerj.16380)

[![DOI](https://zenodo.org/badge/196379320.svg)](https://zenodo.org/badge/latestdoi/196379320)

Seq2science is the attempt of the *van heeringen lab* to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our [docs](https://vanheeringen-lab.github.io/seq2science/) for help with installation, how to run it, and best practices.

![alt text](https://vanheeringen-lab.github.io/seq2science/_static/seq2science.png "seq2science")

Our supported workflows:

* [Downloading of fastq](https://vanheeringen-lab.github.io/seq2science/content/workflows/download_fastq.html)

* [Alignment](https://vanheeringen-lab.github.io/seq2science/content/workflows/alignment.html)

* [ATAC-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/atac_seq.html)

* [RNA-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html)

* [ChIP-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/chip_seq.html)

* [scATAC-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/scatac_seq.html)

* [scRNA-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/scrna_seq.html)

## New users

Information for new users, such as how to install and configure can be found in our [getting started](https://vanheeringen-lab.github.io/seq2science/content/gettingstarted.html) page, and our [Frequently Asked Questions (FAQ)](https://vanheeringen-lab.github.io/seq2science/content/faq.html) section. 

## Feedback

Anything not working as expected? Please reach out to us via our [issues](https://github.com/vanheeringen-lab/seq2science/issues) page and we'll try to help you as soon as possible!

## Cite us

van der Sande M, Frölich S, Schäfers T, Smits JGA, Snabel RR, Rinzema S, van Heeringen SJ. 2023. Seq2science: an end-to-end workflow for functional genomics analysis. PeerJ 11:e16380 https://doi.org/10.7717/peerj.16380