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Attribute
Research Tooling & Frameworks

Snakemake

Snakemake Community (Köster Lab)
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CategoryResearch Tooling & Frameworks
CompanySnakemake Community (Köster Lab)
PriceFree Open Source
StatusStatus not confirmed
AvailabilityAvailable via Bioconda and PyPI
Last checked20/09/2026
FeaturesPython-based rule syntax making pipelines readable and modular, Seamless scaling from single workstations to compute clusters (SLURM, PBS) and cloud environments, Automatic tracking of software dependencies via Conda environments and container images, Integrated reporting tools generating interactive HTML execution and benchmark reports
Entry typeOpen Source Software
Access modeOpen Source
AI roleWorkflow Orchestration & Reproducibility
Input dataNot recorded
Output dataNot recorded
Licence conditionsMIT License
Commercial eligibilityPermissive open source release
Compute requirementsStandard Python environment (runs on laptop or HPC cluster)
ValidationNot recorded
TypeWorkflow management engine
Intended useNot recorded
CompatibilityNot recorded
ManufacturerSnakemake Contributors / University of Duisburg-Essen
Biological applicationGenomic variant calling, RNA-seq analysis, metagenomics, and multi-omics pipelines
Research workflowDefine rules with inputs, outputs, and shell commands -> execute with automated DAG resolution
Evidence levelPeer-reviewed publication (Bioinformatics 2012 / F1000Research 2021) with wide adoption
Integration evidencehttps://snakemake.github.io
Laboratory handoffAutomates analysis pipelines from raw instrument data to final summary tables