Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a comprehensive software package developed in our lab for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing data. MiModD was designed specifically to enable biologists/geneticists with limited bioinformatical knowledge to analyze genome-wide sequencing data of their preferred organism on standard desktop computers.
The software supports:
- – short-reads alignment from different input formats (fastq and gzipped fastq, SAM, BAM)
- – conversion between input formats and annotation with run metadata
- – variant calling (SNPs and indels)
- – variant post-processing, including filtering and annotation
- – deletion calling (currently only for paired-end data)
- – mapping-by-sequencing analyses and variant linkage plots similar to and compatible with CloudMap on your local computer.
- – NEW: replot old CloudMap data on our public NacreousMap server to get ~20x smaller and faster loading pdfs than those produced by CloudMap
MiModD is free and open-source (released under GPLv3) and runs under Linux and Mac OS X (10.9 through 10.11) with minimal software requirements.
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.
Detailed information on installation, usage and hardware requirements can be found in the user guide. If you have questions that are not answered there, we will be happy to assist you.
The package source code, example datasets and other downloads are available from the project’s homepage at sourceforge.