RT Journal Article
SR Electronic
T1 snakePipes enable flexible, scalable and integrative epigenomic analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 407312
DO 10.1101/407312
A1 Vivek Bhardwaj
A1 Steffen Heyne
A1 Katarzyna Sikora
A1 Leily Rabbani
A1 Michael Rauer
A1 Fabian Kilpert
A1 Andreas S Richter
A1 Devon P Ryan
A1 Thomas Manke
YR 2018
UL http://biorxiv.org/content/early/2018/09/04/407312.abstract
AB The scale and diversity of epigenomics data has been rapidly increasing and ever more studies now present analyses of data from multiple epigenomic techniques. Performing such integrative analysis is time-consuming, especially for exploratory research, since there are currently no pipelines available that allow fast processing of datasets from multiple epigenomic assays while also allow for flexibility in running or upgrading the workflows. Here we present a solution to this problem : snakePipes, which can process and perform downstream analysis of data from all common epigenomic techniques (ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq) in a single package. We demonstrate how snakePipes can simplify integrative analysis by reproducing and extending the results from a recently published large-scale epigenomics study with a few simple commands. snakePipes are available under an open-source license at https://github.com/maxplanck-ie/snakepipes.