Snakemake—a scalable bioinformatics workflow engine

Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred mul...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 28; no. 19; pp. 2520 - 2522
Main Authors: Köster, Johannes, Rahmann, Sven
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 01.10.2012
Subjects:
Biological and medical sciences
Computational Biology - methods
Electronic Data Processing
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Programming Languages
Software
Workflow
Scalability
Workflow
Bioinformatics
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Summary:Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. Availability:  http://snakemake.googlecode.com. Contact:  johannes.koester@uni-due.de
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/bts480