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MiModD 0.1.2

Mutation Identification in Model Organism Genomes using Desktop PCs

Package Documentation

Latest Version: 0.1.5.2

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 memory requirements depend on the genome size of the organism that is analyzed. As a rule of thumb you will need a minimum of 8 GB RAM (recommended: 16 GB) to analyze WGS data from typical invertebrate model organisms like Drosophila and C. elegans and between 16 and 32 GB RAM for working with small vertebrate genomes like that of several fish species (e.g., Medaka, pufferfish, zebrafish). See our compilation of hardware requirements for more details on this topic and additional recommendations.

MiModD runs on LINUX and Mac OS systems, requires Python3.2 or higher and, additionally, 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) for variant annotation. If you are prepared to set up your own local Galaxy server , you can integrate MiModD into it with a single command and profit from a graphical user interface and the possibility to turn your machine into an in-house server for WGS analysis.

Obtaining and installing MiModD

You can download the most recent version of MiModD from http://sourceforge.net/projects/mimodd . Installation instructions (covering also the installation of all required software) can be found in the included INSTALL file or here .

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.

 
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