centroid

tool to determine optimal refrerence genome given a set of fasta files

Getting Started

Prerequisites

What dependencies you need to run centroid.py

python3.6+
Mash

Installing Dependencies

Installing python3.6+ First, check your version of python

$ python -v

If you don't have python3.6+, use Anaconda to install:

$ sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
$ wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
$ bash Anaconda3-2019.10-Linux-x86_64.sh
$ source ~/.bashrc

Installing Mash

If you don't have Mash installed and set to your path, do the following:

$ wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
$ tar -xvf mash-Linux64-v2.2.tar
$ rm -rf mash-Linux64-v2.2.tar
$ export PATH="mash-Linux64-v2.2/:$PATH"

Installing centroid

To get centroid, clone this repository:

$ git clone https://github.com/stjacqrm/centroid.git

There's also a containerized version on dockerhub. If you go this route, you won't have to worry about having the dependencies installed (just docker).

Running centroid

To run centroid if you cloned the repository:

$ ./centroid.py /path/to/assemblies/

To run centroid if you're using the docker container:

$  docker run --rm=True -u $(id -u):$(id -g) -v $PWD:/data staphb/centroid centroid.py assemblies/

Authors

This script was originally written by Richard Stanton. I just made incredibly minor modifications for it to run using python3.6+ and to produce an output file as well as printing to the command line.

• Richard Stanton - Actual author - rastanton

• Rachael St. Jacques - Modifier and host for code - stjacqrm