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MiModD 0.1.0

Mutation Identification in Model Organism Genomes using Desktop PCs

Package Documentation

Latest Version: 0.1.2.1

MiModD (Mutation Identification in Model Organism Genomes on Desktop PCs) is a software package for the analysis of whole-genome sequencing (WGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned WGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is designed to shield (especially unexperienced) users from much of the internals of the underlying alignment and variant calling tools and to avoid many of the pitfalls of using those tools separately from the command line. The intention behind MiModD is to bring WGS data analysis from specialized bioinformatics departments to regular genetics labs and to enable geneticists to analyze WGS data on their own without the help of a trained bioinformatician.

Hardware and software requirements

MiModD is designed to run on regular desktop PCs, but its performance depends strongly on available system resources with installed memory being the most critical component. In general, more memory will allow you to work with larger genomes, while a faster processor will reduce analysis times. We recommend an Intel i7 processor and at least 16 GB RAM for good performance for invertebrate model organisms like Drosophila and C. elegans. If you intend to use MiModD on small vertebrate genomes like those of the puffer fish or zebra fish, you will have to have 32 GB of RAM installed (which is also the maximum memory manageable by the i7 processor). MiModD should run on any UNIX-based operating system including any LINUX distribution and Mac OS. We have tested it on Ubuntu 12.04 and Mac OS X. The package depends on Python3.2 or higher and additionally requires the installation of the external programs SNAP aligner (http://snap.cs.berkeley.edu/), samtools (http://sourceforge.net/projects/samtools) and, optionally, SnpEff (http://snpeff.sourceforge.net).

Obtaining and installing MiModD

You can download the most recent version of MiModD from http://sourceforge.net/projects/mimodd . Installation instructions can be found in the included INSTALL file.

Documentation and help

A detailed documentation of the package including a tutorial for beginners can be found here . 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.

 
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