Module-painter: Fast assessment of modular recombinations in bacteriophages

Citation (Work in progress)

Cédric Arisdakessian, Mahdi Belcaid, Anne Bergeron and Guylaine Poisson Module-painter: Fast assessment of modular recombinations in bacteriophages

Description

Module-painter is a tool for identifying the traces of a parent viral population on a target population. By identifying recombination patterns, it clusters the viruses into subpopulations based on their shared history. Module-painter is composed of two main steps. First, we determine a minimal set of segments from the parent population covering each child’s genome. Second, we identify all recombinations shared by multiple children in order to cluster them into subpopulations.

Install

Dependencies:

• minimap2 (or blastn if --aligner blastn is set)
• python dependencies (see setup.py file)
• (optional) pycairo for graph plotting

git clone https://github.com/Puumanamana/module-painter.git \
&& cd module-painter \
&& pip install .

Basic usage

To use module-painter on your own dataset, you need to provide two mandatory arguments: - The viral population (list of fasta files) - The regex patterns or keywords identifying the children population (unless the --rotate-parent flag is set, in which case the parent population rotates among all input fasta files (leave one out strategy)

Example:

module-painter run -p data/*.fasta -c children

module-painter run -p data/*.fasta --rotate-parent

For a comprehensive list of all options, see the command help:

module-painter run -h

Contribute

• Issue Tracker: github
• Source Code: github