snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Vivek Bhardwaj; Steffen Heyne; Katarzyna Sikora; Leily Rabbani; Michael Rauer; Fabian Kilpert; Andreas S Richter; Devon P Ryan; Thomas Manke

doi:10.1093/bioinformatics/btz436

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Bioinformatics. 2019 Nov 1;35(22):4757-4759. doi: 10.1093/bioinformatics/btz436.

Authors

Vivek Bhardwaj^{1

2}, Steffen Heyne¹, Katarzyna Sikora¹, Leily Rabbani¹, Michael Rauer¹, Fabian Kilpert³, Andreas S Richter⁴, Devon P Ryan¹, Thomas Manke¹

Affiliations

¹ Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
² Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
³ Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany.
⁴ Genedata AG, 4053 Basel, Switzerland.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epigenomics*
Exome Sequencing
RNA-Seq
Software*
Workflow