A flexible and modular pipeline for metagenomic analysis.
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:
- Reads preprocessing
- Taxonomic and functional profiling
- Taxonomic binning
- 16S rDNA extraction
- Genome assembly
- Assembly evaluation
- Genome binning
- Bins refinement and assessment
There are two prerequisites for running Metabiome:
- Miniconda installed in Linux systems.
- Metagenomic samples to be analyzed.
Download or clone this repository and run install.sh in the command line:
cd Metabiome/
bash install.shThe installation script will create Conda environments with all the software you can use with Metabiome.
Metabiome can be invoked like so:
metabiome --helpSee the documentation for further details.
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.
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.
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
Authors: Cristian Grisales-Vargas, Estefany Lorenzana, Juan Camilo Arboleda, Juan Esteban Pérez Jaramillo.