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Sunbeam: a robust, extensible metagenomic sequencing pipeline

Tests Documentation Status DockerHub DOI:10.1186/s40168-019-0658-x

Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin privileges, and can be deployed on most Linux workstations and clusters. Sunbeam was designed to be modular and extensible, allowing anyone to build off the core functionality. To read more, check out our paper in Microbiome.

Sunbeam currently automates the following tasks:

More extensions can be found at

To get started, see our documentation!

If you use the Sunbeam pipeline in your research, please cite:

EL Clarke, LJ Taylor, C Zhao, A Connell, J Lee, FD Bushman, K Bittinger. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome 7:46 (2019)

See how people are using Sunbeam: