dRep

Reduces the computational time for pair-wise genome set comparisons by orders of magnitude. dRep sequentially applies an inaccurate estimation of genome distance and a slow but accurate measure of average nucleotide identity. It is easy to use, highly customizable, and parallelizable. The tool can perform rapid pairwise genomic comparisons (without de-replication) to enable visualization of the degree of similarity among groups of similar genomes.

dRep statistics

Citations per year

Tool usage distribution map

This map represents all the scientific publications referring to dRep per scientific context

Associated diseases

Popular tool citations

Whole genome alignment

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Protocols

dRep specifications

Desktop

Information

Unique identifier	OMICS_16085
Name	dRep
Software type	Package/Module
Interface	Command line interface
Restrictions to use	None
Operating system	Unix/Linux
Programming languages	Python
Computer skills	Advanced
Version	0.3.4
Stability	Stable
Requirements	Mash, Nucmer, CheckM, Prodigal, gANI, Centrifuge
Maintained	Yes

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Versioning

No version available

Documentation

Documentation: http://drep.readthedocs.io/en/master/
Issues: https://github.com/MrOlm/drep/issues

Maintainer

Jillian Banfield

Publication for dRep

DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.

2017 ISME J

PMCID: 5702732

PMID: 28742071

DOI: 10.1038/ismej.2017.126

dRep citations

(2)

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

2018

MBio

PMCID: 5893878

PMID: 29636439

DOI: 10.1128/mBio.00441-18

[…] taxonomic assignments. In order to identify cases in which the same bacterial strain was present in multiple samples, subspecies groups were further analyzed with the ANIm algorithm () implemented in dRep (). […]

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

2018

mSystems

PMCID: 5758725

PMID: 29359195

DOI: 10.1128/mSystems.00123-17

See protocol

[…] was calculated and used to run concoct () with default parameters on all individual assemblies and coassemblies. To remove redundant bins, all bins recovered from each infant were dereplicated using dRep () v0.4.0 with the following command: dRep dereplicate_wf--S_algorithm gANI -comp 50 -con 25 -str 25 -l 50000 -pa 0.9 -nc.1.Using Bowtie2 (), the reads from each sample were mapped to the set of […]

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