Tools for Mutation Identification in Model Organism Genomes using Desktop PCs
Project description
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 the genetic mutations present in an organism starting from just raw WGS read data and a reference genome without the help of a trained bioinformatician.
MiModD is designed for good performance on standard hardware and enables WGS data analysis for most model organisms on regular desktop PCs.
MiModD can be installed under Linux and Mac OS 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 and software requirements
Hardware
MiModD performs very well on standard desktop PCs provided that they meet the memory requirements imposed by the genome size of the organism that is analyzed.
8 GB RAM are required (16 GB recommended) to analyze WGS data from typical invertebrate model organisms like Drosophila and C. elegans and between 16 and 32 GB RAM are necessary for working with small vertebrate genomes like that of several fish species (e.g., Medaka, pufferfish, zebrafish).
Of note, these memory requirements concern only the initial mapping step of WGS analysis. Variant calling, annotation and filtering steps starting from aligned reads files can all be carried out with MiModD with minimal memory requirements.
See our compilation of hardware requirements at http://mimodd.readthedocs.org/en/latest/hardware.html for more details on this topic and additional hardware recommendations.
Software
MiModD runs under LINUX and Mac OS and requires Python 3.2 or higher.
Installation of SnpEff (http://snpeff.sourceforge.net) for variant annotation, which in turn requires Java, is optional.
If you would like to set up your own local Galaxy server, to enjoy a graphical user interface and the possibility to turn your machine into an in-house server for WGS analysis, you will need Python 2.6 or 2.7 installed alongside Python 3. You will also need Mercurial to clone the current Galaxy source code as the basis of the installation.
Obtaining and installing MiModD
Installation instructions (covering also the installation of all required and optional software) can be found in the INSTALL file included in this distribution.
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 mimodd@googlegroups.com.
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Source Distribution
Built Distributions
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