Installation

Using pip

To install dRep, simply run

$ pip install drep

OR

$ git clone https://github.com/MrOlm/drep.git

$ cd drep

$ pip install .

That’s it!

Pip is a great package with many options to change the installation parameters in various ways. For details, see pip documentation

Dependencies

dRep requires other programs to run. Not all dependencies are needed for all operations

To check which dependencies are installed on your system and accessible by dRep, run

$ dRep bonus testDir --check_dependencies

Near Essential

  • Mash - Makes primary clusters (v1.1.1 confirmed works)
  • MUMmer - Performs ANIm comparison method (v3.23 confirmed works)

Recommended

  • CheckM - Determines contamination and completeness of genomes (v1.0.7 confirmed works)
  • gANI (aka ANIcalculator) - Performs gANI comparison method (v1.0 confirmed works)
  • Prodigal - Used be both checkM and gANI (v2.6.3 confirmed works)

Accessory

  • Centrifuge - Performs taxonomic assignment of bins (v1.0.3 confirmed works)

Programs need to be installed to the system path, so that you can call them from anywhere on your computer.

Note

If you already have information on your genome’s completeness and contamination, you can input that to dRep without the need to install checkM (see Advanced Use))

CheckM

CheckM is the program that dRep uses to calculate completeness and contamination. It’s not required for all dRep commands, but if you’d like to de-dereplicate your genome set using completeness and contamination it is required. It takes a bit of work to install (including setting a root directory and downloading a reference database). Installation instructions can be found here <https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm>