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https://github.com/maxplanck-ie/snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
https://github.com/maxplanck-ie/snakepipes

atac-seq bisulfite-sequencing chip-seq hi-c ngs rna-seq snakemake workflow

Last synced: about 1 month ago
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Customizable workflows based on snakemake and python for the analysis of NGS data

Host: GitHub
URL: https://github.com/maxplanck-ie/snakepipes
Owner: maxplanck-ie
License: mit
Created: 2016-03-23T17:23:31.000Z (almost 9 years ago)
Default Branch: master
Last Pushed: 2024-04-12T13:19:25.000Z (8 months ago)
Last Synced: 2024-04-12T23:34:22.904Z (8 months ago)
Topics: atac-seq, bisulfite-sequencing, chip-seq, hi-c, ngs, rna-seq, snakemake, workflow
Language: Python
Homepage: http://snakepipes.readthedocs.io
Size: 39.7 MB
Stars: 369
Watchers: 19
Forks: 85
Open Issues: 29
Metadata Files:
- Readme: README.rst
- License: LICENSE

Awesome Lists containing this project

README

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snakePipes

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.. image:: https://readthedocs.org/projects/snakepipes/badge/?version=latest

    :target: http://snakepipes.readthedocs.io/en/latest/?badge=latest

    :alt: Documentation Status

.. image:: https://travis-ci.org/maxplanck-ie/snakepipes.svg?branch=develop

    :target: https://travis-ci.org/maxplanck-ie/snakepipes

    :alt: Build Staus

.. image:: https://zenodo.org/badge/54579435.svg

    :target: https://zenodo.org/badge/latestdoi/54579435

    :alt: Citation

snakePipes are flexible and powerful workflows built using `Snakemake `__ that simplify the analysis of NGS data.

.. image:: ./docs/content/images/snakePipes_small.png

   :scale: 20 %

   :width: 100 px

   :height: 100 px

   :align: right

Workflows available

--------------------

- DNA-mapping*

- ChIP-seq*

- mRNA-seq*

- noncoding-RNA-seq*

- ATAC-seq*

- scRNA-seq

- Hi-C

- Whole Genome Bisulfite Seq/WGBS

**(*Also available in "allele-specific" mode)**

Installation

-------------

Snakepipes is a set of Snakemake workflows which use conda for installation and dependency resolution, so you will need to `install conda `__ first.

Afterward, simply run the following:

``conda install mamba -c conda-forge && mamba create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes``

This will create a new conda environment called "snakePipes" into which snakePipes is installed. You will then need to create the conda environments needed by the various workflows. To facilitate this we provide the `snakePipes` commands:

* ``conda activate snakePipes`` to activate the appropriate conda environment.

* ``snakePipes createEnvs`` to create the various environments.

Indices and annotations needed to run the workflows could be created by a simple command :

``createIndices --genomeURL  --gtfURL  -o  ``

where `name` refers to the name/id of your genome (specify as you wish).

A few additional steps you can then take:

1. **Modify/remove/add the organism yaml files appropriately** : these yaml files would contain location of appropriate

GTF files and genome indexes corresponding to different organisms. The location of these files after installation can be

found using ``snakePipes info`` command.

2. **Modify the cluster.yaml file appropriately** : This yaml file contains settings for your cluster scheduler (SGE/slurm).

Location revealed using ``snakePipes info`` command.

Documentation

--------------

For detailed documentation on setup and usage, please visit our `read the docs page `__.

Citation

-------------

If you adopt/run snakePipes for your analysis, cite it as follows :

Bhardwaj, Vivek, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, and Thomas Manke. 2019. “snakePipes: Facilitating Flexible, Scalable and Integrative Epigenomic Analysis.” Bioinformatics , May. `doi:10.1093/bioinformatics/btz436 `__

Note

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SnakePipes are under active development. We appreciate your help in improving it further. Please use issues to the GitHub repository for feature requests or bug reports.