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Snakemake | A scalable bioinformatics workflow engine

Provides an execution environment with a clean and readable specification language to reduce the complexity of creating workflows. Snakemake is a workflow engine inspired by the build system GNU Make. The software interoperates with any installed tool or available web service with well-defined input and output (file) formats. Apart from running on single machines, Snakemake contains a generic mechanism that allows the execution of jobs on a batch system or a compute cluster engine.

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2 user reviews

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2 user reviews

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Samuel Lampa's avatar image Samuel Lampa's country flag

Samuel Lampa

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A top-quality software that is really helpful for low- to medium complexity workflows, especially where you might want to re-generate certain outputs based on updated inputs.

For really complex workflows, such as when involving multiple nested parameter sweeps and/or cross-validation constructs implemented in the workflow layer, it can get a bit complicated to figure out how to write that, and something more dataflow-like like NextFlow might be preferrable in such cases.

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

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A useful pipeline generator in python that allows to create modules (rules) for each step. A little bit confusing at the beginning if one doesn't know make but very powerful at the end. An important point : Snakemake allows graphics workflow output.

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Snakemake classification

Snakemake specifications

Unique identifier:
OMICS_02299
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
License:
MIT License
Stability:
Stable
Maintained:
Yes
Software type:
Framework/Library
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Requirements:
BWA, SAMtools, BCFtools, Graphviz, PyYAML, Docutils

Snakemake distribution

versioning

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Snakemake support

Documentation

Maintainer

  • Johannes Köster <>

Credits

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Publications

Institution(s)

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and Paediatric Oncology, University Childrens Hospital, Essen, Germany

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