Metabiome

A flexible and modular pipeline for metagenomic analysis.

About Metabiome

Metabiome is a bioinformatic pipeline for metagenomic analysis. It consists of a series of wrapper scripts written in Bash. It is also contained in Conda environments to ease its use. Metabiome includes several features of common microbiome analysis:

1. Reads preprocessing
2. Taxonomic and functional profiling
3. Taxonomic binning
4. 16S rDNA extraction
5. Genome assembly
6. Assembly evaluation
7. Genome binning
8. Bins refinement and assessment

Pipeline

Prerequisites for running Metabiome

There are two prerequisites for running Metabiome:

1. Miniconda installed in Linux systems.
2. Metagenomic samples to be analyzed.

Installation

Download or clone this repository and run install.sh in the command line:

cd Metabiome/
bash install.sh

The installation script will create Conda environments with all the software you can use with Metabiome.

Basic usage

Metabiome can be invoked like so:

metabiome --help

See the documentation for further details.

Contribute to Metabiome

If you want to contribute to Metabiome, you should fork the project. Then, make your desired changes and submit a pull request in order to be evaluated by the current developers.

Submit an issue

If you have problems or suggestions regarding Metabiome, please submit an issue on Metabiome issues. Also, please search the previous issues (if any) before submiting a new one in order to avoid duplications.

Ask for help

If you have questions about how to use Metabiome, or are interested in active collaboration of this project, do not hesitate to contact:

Cristian Grisales-Vargas
Estefany Lorenzana
Juan Camilo Arboleda

Acknowledgements

Authors: Cristian Grisales-Vargas, Estefany Lorenzana, Juan Camilo Arboleda, Juan Esteban Pérez Jaramillo.