Magnetosome gene cluster annotation, screening and mapping tool
Project description
magcluster
Magnetosome gene cluster annotation, screening and mapping tool
Installation
We recommend creating a new environment for the magcluster release being installed through conda.
wget https://github.com/RunJiaJi/magcluster/releases/download/0.1.3/magcluster-0.1.3.yml
conda env create -n magcluster --file magcluster-0.1.3.yml
# OPTIONAL CLEANUP
rm magcluster-0.1.3.yml
Alternatively, you can install magcluster through pip in an existing environment. In this way, please make sure you have prokka installed.
#Prokka installation
conda install -c conda-forge -c bioconda -c defaults prokka
pip install magcluster
General Usage
usage: magcluster [options]
Magnetosome Gene Cluster Analysis Tool
optional arguments:
-h, --help show this help message and exit
-v, --version show magcluster version number and exit
Options:
{prokka,mgc_screen,clinker}
prokka Genome annotation with Prokka
mgc_screen Magnetosome gene cluster screening with magscreen
clinker Magnetosome gene cluster mapping with Clinker
General usage
-------------
Magnetosome gene annotation:
$ magcluster prokka XXX.fa
Magnetosome gene screen:
$ magcluster mgc_screen XXX.gbk
Magnetosome gene cluster mapping:
$ magcluster clinker XXX_screened.gbk
Runjia, 2021
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