:warning: This software is still in early development

noary

A lightweight nucleotide bacterial ortholog clustering tool

Introduction

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.

Quick Start

% noary --version
noary 0.1.2

Installation

Conda

Install Conda or Miniconda:

conda install -c conda-forge -c bioconda -c defaults noary # COMING SOON

Homebrew

Install HomeBrew (Mac OS X) or LinuxBrew (Linux).

brew install brewsci/bio/noary # COMING SOON

Source

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

Dependencies

• perl >= 5.26
• cd-hit-est from CD-HIT >= 4.8
• blastn from BLAST+ >= 2.7
• mcl >= 14

License

noary is free software, released under the GPL 3.0.

Issues

Please submit suggestions and bug reports to the Issue Tracker

Author

Torsten Seemann