From 57092e0c6e0ce6c34c3c0bb183c0702fe8edf620 Mon Sep 17 00:00:00 2001 From: Matt Olm Date: Fri, 8 Dec 2017 15:23:45 -0800 Subject: [PATCH] changed readme --- README.md | 45 ++++++++++++++++++++++++++++++++++++++------- 1 file changed, 38 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 12262a1..9650661 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,42 @@ # dRep -De-replication of microbial genomes. -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. -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/) -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) + +Open source pre-print publication is available at +[bioRxiv](https://doi.org/10.1101/108142) + +## Installation with pip +``` +$ pip install drep +``` + +## Quick start + +### Genome comparison: +``` +$ dRep compare_wf output_directory -g path/to/genomes/*.fasta +``` + +### Genome de-replication: +``` +$ dRep dereplicate_wf outout_directory -g path/to/genomes/*.fasta +``` + +## 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 + +### 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 + +### Accessory +* [Centrifuge](https://omictools.com/centrifuge-tool) can be used to perform rough taxonomic assignment of bins