MGLEX 0.2.1

MGLEX - MetaGenome Likelihood EXtractor

This Python Package provides a probabilistic model to classify nucleotide sequences in metagenome samples. It was developed as a framework to help researchers to reconstruct individual genomes from such datasets using custom workflows and to give developers the possibility to integrate the model into their programs.

• Free software: GPLv3 license

• Source code: https://github.com/fungs/mglex

• Documentation: https://mglex.readthedocs.io

Features

• Integrates nucleotide composition, multi-sample coverage and taxonomic annotation

• Learns a model in linear time with respect to the number of input sequences

• Classifies novel sequences in linear time

• Calculates likelihood and p-values

• Calculates probabilistic distances between genome bins

Dependencies

MGLEX is a Python 3 package, it does not run with Python 2 versions. It depends on

• NumPy

• SciPy (for few functions)

• docopt

Installation

Install dependencies with Debian/Ubuntu & Python-Virtualenv

We show how to install MLGEX under Debian and Ubuntu, but other platforms are similar.

You can simply install the requirements as system packages.

sudo apt install python3 python3-numpy python3-scipy

We recommend to create a Python virtual installation enviroment for MGLEX. In order to do so, install the venv package for your Python version (e.g. the Debian package python3.4-venv), if not included (or use virtualenv). The following command will make use of the installed system packages.

python3 -m venv --system-site-packages mglex-env
source mglex-env/bin/activate

Install dependencies with Conda

Similarly, you can use Anaconda or Conda to prepare an environment with the dependencies and activate it.

conda create -n mglex-env -c conda-forge numpy scipy docopt python=3
source activate mglex-env

Install MGLEX Python package

MGLEX is deposited on the Python Package Index and we recommend to install it via pip.

python -m pip install mglex

Credits

This package was created using NumPy by Johannes Dröge at the Computational Biology of Infection Research Group at the Helmholtz Centre for Infection Research, Braunschweig, Germany.

Please cite:

Dröge J, Schönhuth A, McHardy AC. (2017) A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science 3:e117 https://doi.org/10.7717/peerj-cs.117