Welcome to Sunbeam


Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. Sunbeam requires a reasonably modern GNU/Linux computer with bash, Python 3.7+, internet access (to retrieve dependencies), and at least 4Gb of RAM. RAM and disk space requirements may increase depending on the databases and tasks you choose to run, and the size of your data. For more information, check out the Sunbeam paper in Microbiome.

Sunbeam currently automates the following tasks:

  • Quality control, including adaptor trimming, host read removal, and quality filtering;

  • Decontamination of host-contaminated reads

Sunbeam was designed to be modular and extensible. We have Sunbeam Extensions available that handle assembly, annotation, read alignments, taxonomic classifications, and more.

To get started, see our Quickstart Guide!

For lots of examples of common Sunbeam use cases, see our Sunbeam Examples.

If you use Sunbeam in your research, please cite:

EL Clarke, LJ Taylor, C Zhao et al. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome 7:46 (2019)