Quick Start¶

The functionality of dRep is broken up into modules. To see a list of the available modules, check the help:

$ dRep -h
                ...::: dRep v3.0.0 :::...

  Matt Olm. MIT License. Banfield Lab, UC Berkeley. 2017 (last updated 2020)

  See https://drep.readthedocs.io/en/latest/index.html for documentation
  Choose one of the operations below for more detailed help.

  Example: dRep dereplicate -h

  Commands:
    compare            -> Compare and cluster a set of genomes
    dereplicate        -> De-replicate a set of genomes
    check_dependencies -> Check which dependencies are properly installed

Dereplication¶

Dereplication is the process of identifying groups of genomes that are the “same” in a genome set and identifying the “best” genome from each set. How similar genomes need to be to be considered “same” and how the “best” genome is chosen are study-specific decisions that can be adjusted (see Important Concepts)

To dereplicate a set of genomes, run the following command:

$ dRep dereplicate outout_directory -g path/to/genomes/*.fasta

This will automatically de-replicate the genome list and produce lots of information about it.

Genome comparison¶

dRep is able to perform rapid genome comparisons for a group of genomes and visualize their relatedness. For example:

$ dRep compare output_directory -g path/to/genomes/*.fasta

For help understanding the output, see Example Output

To change the comparison parameters, see Important Concepts