Fast and accurate Average Genome Size and 16S rRNA gene Average Copy Number computation in metagenomic data

Here, we present the ags.sh and acn.sh tools dedicated to the computation of the Average Genome Size (AGS) and 16S rRNA gene Average Copy Number (ACN), respectively. The ags.sh and acn.sh tools compute these metagenomic traits based on the (ultra-fast) annotation of 35 universally distributed single-copy genes in unassembled metagenomic data.

Citation

Pereira-Flores, E., Glöckner F. O., and Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinformatics. 2019;20(1):453. doi:10.1186/s12859-019-3031-y.

Installation

Before running ags.sh and acn.sh tools, it is necessary to install docker.

Then just clone the GitHub repository:

git clone https://github.com/pereiramemo/AGS-and-ACN-tools.git

The ags.sh and acn.sh are distributed in two different docker images which will be downloaded automatically from dockerhub the first time you run the run_ags.sh and run_acn.sh scripts.

Go to the wiki page to find the documentation, more in detail installation instructions, and a getting started tutorial.