polyfix

Introduction

Genomes assembled from Nanopore data are imperfect. Even at 99.9% consensus accuracy there remains ~1 error per 1000 bp. Given a typical bacterial gene is ~1000 bp, this means 1 error per gene. The most common error mode in Nanopore is indels, usually around homopolymer regions. This results in a frame-shift in the gene, causing annotation tools like Prokka to find two partial genes instead of one intact gene.

Ideally one would also sequence with Illumina and polish the assembly, as Illumina data does not suffer from homopolymer issues. However, if you are unable to do that, polyfix is designed to take your draft Nanopore assembly and compare it to one or more "trusted reference" genomes, and polish out likely homopolymer errors to remove the frame-shifts.

Quick Start

% polyfix --version
polyfix 0.0.1

% polyfix --help

Installation

Conda

Install Conda or Miniconda:

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

Homebrew

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

brew install brewsci/bio/polyfix  # COMING SOON

Source

This will install the latest version direct from Github. You'll need to add the polyfix bin directory to your $PATH, and also ensure all the dependencies are installed.

cd $HOME
git clone https://github.com/tseemann/polyfix.git
$HOME/polyfix/bin/polyfix --help

Dependencies

• perl >= 5.26

License

polyfix is free software, released under the GPL 3.0.

Issues

Please submit suggestions and bug reports to the Issue Tracker

Author

Torsten Seemann