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magpurify website  

This package uses a combination of different features and algorithms to identify contamination in metagenome-assembled genomes (MAGs). Contamination is defined as contigs that originated from a different species relative to the dominant organism present in the MAG.

Each module in the software package was designed to be highly specific. This means that not all contamination (contigs from other species) will be removed, but very few contigs will be incorrectly removed. Feel free to modify the default parameters for more sensitive detection of contamination.

Environment Modules

Run module spider magpurify to find out what environment modules are available for this application.

System Variables

  • HPC_MAGPURIFY_DIR - installation directory
  • MAGPURIFYDB - database directory


If you publish research that uses magpurify you have to cite it as follows:

Nayfach, Stephen, et al. "New insights from uncultivated genomes of the global human gut microbiome." Nature 568.7753 (2019): 505-510.