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# dRep | ||
De-replication of microbial genomes. | ||
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Manual and installation instructions available at ReadTheDocs: | ||
[link to documentation](http://drep.readthedocs.io/en/master/) | ||
dRep is a 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. | ||
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Publication available at ISMEJ: | ||
[link to publication](http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2017126a.html) | ||
Manual, installation instructions, and API are at available at | ||
[ReadTheDocs](http://drep.readthedocs.io/en/master/) | ||
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Open source pre-print available at bioRxiv: | ||
[link to pre-print](https://doi.org/10.1101/108142) | ||
Publication is available at | ||
[ISMEJ](http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2017126a.html) | ||
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Open source pre-print publication is available at | ||
[bioRxiv](https://doi.org/10.1101/108142) | ||
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## Installation with pip | ||
``` | ||
$ pip install drep | ||
``` | ||
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## Quick start | ||
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### Genome comparison: | ||
``` | ||
$ dRep compare_wf output_directory -g path/to/genomes/*.fasta | ||
``` | ||
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### Genome de-replication: | ||
``` | ||
$ dRep dereplicate_wf outout_directory -g path/to/genomes/*.fasta | ||
``` | ||
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## Dependencies | ||
### Required | ||
* [Mash](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x) is used to repadily compare all genomes in a pair-wise manner | ||
* [MUMmer](http://mummer.sourceforge.net/) is used to perform more actuate comparisons between genomes which are shown to be similar with Mash | ||
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### Recommended | ||
* [CheckM](http://ecogenomics.github.io/CheckM/) is used to determine the contamination and completeness of genomes (used during de-replication) | ||
* [gANI (aka ANIcalculator)](https://ani.jgi-psf.org/html/download.php?) is an optional alternative to MUMmer | ||
* [Prodigal](http://prodigal.ornl.gov/) is a dependency of both checkM and gANI | ||
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### Accessory | ||
* [Centrifuge](https://omictools.com/centrifuge-tool) can be used to perform rough taxonomic assignment of bins |