MiModD 0.1.9

Tools for Mutation Identification in Model Organism Genomes using Desktop PCs

MiModD is an integrated solution for efficient and user-friendly analysis of whole-genome sequencing (WGS) data from laboratory model organisms. It enables geneticists to identify and annotate the genetic mutations present in an organism and to perform linkage analyses to identify variants responsible for mutant phenotypes.

MiModD is designed to enable biologists/geneticists with limited bioinformatical knowledge to analyze their genome-wide sequencing data without the help of a trained bioinformatician.

Requirements

MiModD can be installed under Linux and macOS (10.9-10.13) with minimal software requirements and a simple setup procedure. As a standalone package it can be used from the command line, but can also be integrated seamlessly and easily into any local installation of a Galaxy bioinformatics server providing a graphical user interface, database management of results and simple composition of analysis steps into workflows.

Hardware

For many use cases MiModD performs very well on standard desktop PCs and notebooks. Detailed information on hardware requirements and recommendations is available at http://mimodd.readthedocs.io/en/latest/hardware.html.

Software

MiModD requires Python 3.3 or higher. Python 2 is not supported.

Obtaining and installing MiModD

MiModD is pip-installable via:

python3 -m pip install MiModD

Once installed successfully, run:

python3 -m MiModD.config

for basic configuration.

More detailed installation instructions for MiModD, dependencies and recommended additional software can be found in the INSTALL file included in the source distribution or at http://mimodd.readthedocs.io/en/latest/INSTALL.html.

Documentation and help

We have prepared a detailed online documentation of the package including a tutorial for beginners. If you experience problems with any part of MiModD or you think you found a bug in the software, the preferred way of letting us and others know is through posting to the MiModD user group at https://groups.google.com/forum/#!forum/mimodd or via email to [e-mail].