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A toolkit based on snakemake and python for analysis of NGS data
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README.rst

snakePipes

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

./docs/content/images/snakePipes.png

Workflows available

  • DNA-mapping*
  • ChIP-seq*
  • RNA-seq*
  • ATAC-seq*
  • scRNA-seq
  • Hi-C
  • Whole Genome Bisulfite Seq/WGBS

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

Installation

Snakepipes uses conda for installation and dependency resolution, so you will need to install conda first.

Afterward, simply run the following:

conda 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 and register GATK.

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

createIndices --genomeURL <path/url to your genome fasta> --gtfURL <path/url to genes.gtf> -o <output_dir> <name>

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 V, Heyne S, Sikora K, Rabbani L, Rauer M, Kilpert F, et al. snakePipes enable flexible, scalable and integrative epigenomic analysis. bioRxiv. 2018. p. 407312. doi:10.1101/407312

Note

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.

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