安装dRep

https://github.com/MrOlm/drep

https://www.nature.com/articles/ismej2017126/

##

pip install drep

##检查依赖关系

dRep bonus work_directory --check_dependencies

Loading work directory

Checking dependencies

mash.................................... !!! ERROR !!!  (location = None)

nucmer.................................. !!! ERROR !!!  (location = None)

checkm.................................. !!! ERROR !!!  (location = None)

ANIcalculator........................... !!! ERROR !!!  (location = None)

prodigal................................ !!! ERROR !!!  (location = None)

centrifuge.............................. !!! ERROR !!!  (location = None)

nsimscan................................ !!! ERROR !!!  (location = None)

fastANI................................. !!! ERROR !!!  (location = None)

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x

https://github.com/marbl/mash

https://sourceforge.net/projects/mummer/

https://github.com/marbl/Mash/releases

https://github.com/Ecogenomics/CheckM/wiki/Installation

pip install checkm-genome

https://ani.jgi.doe.gov/html/anicalculator.php

sudo gedit .bashrc

prodigal

https://github.com/hyattpd/Prodigal#:~:text=Predicts%20protein-coding%20genes%3A%20Prodigal%20provides%20fast%2C%20accurate%20protein-coding,smoothly%20on%20finished%20genomes%2C%20draft%20genomes%2C%20and%20metagenomes.

sudo apt-get install zlib1g-dev

sudo make install

dRep dereplicate outout_directory -g path/to/genomes/*.fasta