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 extensions available that handle visualization tasks, including contig assembly graphs, read alignments, and taxonomic classifications.
To get started, see our quickstart!
quickstart.rst usage.rst extensions.rst