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 2.6+, internet access (to retrieve dependencies), 4Gb of RAM, and at least 3Gb of disk space. 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;
• Taxonomic assignment of reads to databases using Kraken;
• Assembly of reads into contigs using Megahit;
• Contig annotation using BLAST[n/p] and Diamond;
• Mapping of reads to target genomes; and
• ORF prediction using Prodigal

Sunbeam was designed to be modular and extensible. We have a few pre-built Sunbeam Extensions available that handle visualization tasks, including contig assembly graphs, read alignments, and taxonomic classifications.

To get started, see our Quickstart Guide!

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)