Welcome to Sunbeam

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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 and Mac workstations and clusters.

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/x];
  • 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!