snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
28
01
2019
revised:
29
04
2019
accepted:
23
05
2019
pubmed:
28
5
2019
medline:
2
7
2020
entrez:
29
5
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31134269
pii: 5499080
doi: 10.1093/bioinformatics/btz436
pmc: PMC6853707
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4757-4759Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
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