snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 31134269.
- Also identified by DOI 10.1093/bioinformatics/btz436 and PMC identifier 6853707.
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Abstract
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. 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 data are available at Bioinformatics online.
Medical subject headings
- Epigenomics
- Software