Anvio: an analysis and sualization platform for 'omics data

In this extension, we show how easy it is to add downstream analysis to sunbeam pipeline as an extension.

Installation

To install:

sunbeam extend https://github.com/sunbeam-labs/sbx_anvio

Legacy instructions for older Sunbeam versions are below.

Usage

This adds a new rule, all_anvio_scg. Specify this as your target to use Anvio to look at the distributuion of bacterial single-copy genes in this contigs database, and roughly predict the number of genomes in it:

sunbeam run --configfile sunbeam_config.yml --use-conda all_anvio_scg 

The --use-conda flag is required to let Snakemake know that you want to use the sbx_anvio conda environment.

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Installation (legacy instructions for Sunbeam version <3.0)

With your sunbeam conda environment activated,

1. Clone into your Sunbeam directory:

   git clone https://github.com/sunbeam-labs/sbx_anvio sunbeam/extensions/sbx_anvio