dRep
dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
Manual, installation instructions, and API are at available at ReadTheDocs
Publication is available at ISMEJ
Open source pre-print publication is available at bioRxiv
Installation with pip
$ pip install drep
Quick start
Genome comparison:
$ dRep compare output_directory -g path/to/genomes/*.fasta
Genome de-replication:
$ dRep dereplicate outout_directory -g path/to/genomes/*.fasta
Make sure dependencies are properly installed:
$ drep check_dependencies
Dependencies
Required
- Mash is used to rapidly compare all genomes in a pair-wise manner
- MUMmer is used to perform more actuate comparisons between genomes which are shown to be similar with Mash
Optional
- CheckM is used to determine the contamination and completeness of genomes (used during de-replication)
- gANI (aka ANIcalculator) is an optional alternative to MUMmer
- Prodigal is a dependency of both checkM and gANI
Accessory
- Centrifuge can be used to perform rough taxonomic assignment of bins