A robust, extensible metagenomics pipeline
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Readme.md

Sunbeam: a robust, extensible metagenomic sequencing pipeline

CircleCI Documentation Status

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.

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!

To get started, see our documentation!


Changelog:

v1.2.1 (May 24, 2018)

  • Minor bugfixes

v1.2.0 (May 2, 2018)

  • Low-complexity reads are now removed by default rather than masked
  • Bug fixes related to single-end sequencing experiments
  • Documentation updates

v1.1.0 (April 8, 2018)

  • Reports include number of filtered reads per host, rather than in aggregate
  • Static binary dependency for komplexity for easier deployment
  • Remove max length filter for contigs

v1.0.0 (March 22, 2018)

  • First stable release!
  • Support for single-end sequencing experiments
  • Low-complexity read masking via komplexity
  • Support for extensions
  • Documentation on ReadTheDocs.io
  • Better assembler (megahit)
  • Better ORF finder (prodigal)
  • Can remove reads from any number of host/contaminant genomes
  • Semantic versioning checks
  • Integration tests and continuous deployment

Contributors