snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.
- Bhardwaj V Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Heyne S Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Sikora K Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Rabbani L Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Rauer M Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Kilpert F Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany.
- Richter AS Genedata AG, 4053 Basel, Switzerland.
- Ryan DP Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- Manke T Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
- 2019-05-29
Published in:
- Bioinformatics (Oxford, England). - 2019
English
SUMMARY
Due 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 IMPLEMENTATION
snakePipes 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 INFORMATION
Supplementary data are available at Bioinformatics online.
Due 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 IMPLEMENTATION
snakePipes 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 INFORMATION
Supplementary data are available at Bioinformatics online.
- Language
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- English
- Open access status
- hybrid
- Identifiers
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- DOI 10.1093/bioinformatics/btz436
- PMID 31134269
- Persistent URL
- https://folia.unifr.ch/global/documents/251296
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