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Bioinformatics. 2019 May 27. pii: btz436. doi: 10.1093/bioinformatics/btz436. [Epub ahead of print]

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.

Author information

1
Max Planck Institute of Immunobiology and Epigenetics. Stübeweg 51, Freiburg Germany.
2
Faculty of Biology, University of Freiburg, Schänzlestraße 1, Freiburg, Germany.
3
Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, Maria-Goeppert-Str. 1, Lübeck, Germany.
4
Genedata AG, Margarethenstrasse 38, 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:

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.

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