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- Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S Richter, Devon P Ryan, and Thomas Manke.
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Bioinformatics. 2019 Nov 1; 35 (22): 4757-4759.
SummaryDue to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files.Availability And ImplementationsnakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'. Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.Supplementary InformationSupplementary data are available at Bioinformatics online.© The Author(s) 2019. Published by Oxford University Press.
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