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Sunbeam: a robust, extensible metagenomic sequencing pipeline

CircleCI Super-Linter Conda Envs Status Documentation Status 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. To read more, check out our 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/x];
  • Mapping of reads to target genomes; and
  • ORF prediction using Prodigal.

Sunbeam was designed to be modular and extensible. Some extensions have been built for:

  • IGV for viewing read alignments
  • KrakenHLL, an alternate read classifier
  • Kaiju, a read classifier that uses BWA rather than kmers
  • Anvi'o, a downstream analysis pipeline that does lots of stuff!

More extensions can be found at the extension page: https://github.com/sunbeam-labs.

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:


Contributors