A lightweight nucleotide bacterial ortholog clustering tool
If you want to cluster bacterial protein sequences, you usually use Roary the pan-genome pipeline; to incorporate non-coding transcripts you may use PIRATE; and examination of intergenic regions may lead you to Piggy.
Noary tries to fill the niche of nucleotide gene/sequence clustering. It is intended to be a simple tool for use by other more complex pipelines. It was originally conceived with Harry Thorpe when I visited University of Bath, UK in 2017.
% noary --version
noary 0.1.2
conda install -c conda-forge -c bioconda -c defaults noary # COMING SOON
Install HomeBrew (Mac OS X) or LinuxBrew (Linux).
brew install brewsci/bio/noary # COMING SOON
This will install the latest version direct from Github.
You'll need to add the noary bin
directory to your $PATH
,
and also ensure all the dependencies are installed.
cd $HOME
git clone https://github.com/tseemann/noary.git
$HOME/noary/bin/noary --help
perl
>= 5.26cd-hit-est
from CD-HIT >= 4.8blastn
from BLAST >= 2.7mcl
>= 14
noary is free software, released under the GPL 3.0.
Please submit suggestions and bug reports to the Issue Tracker