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.
See also
- Example Output
- to view example output
- Important Concepts
- for guidance changing parameters
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
See also
- Example Output
- to view example output
- Important Concepts
- for guidance changing parameters