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MiModD User Guide — MiModD 0.1.7.3 documentation

MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data. Whom is it for? MiModD was designed specifically to enable biologists/geneticists with limited bioinformatical knowledge to analyze genome-wide sequencing data of their preferred organism on off-the-shelf desktop computers. MiModD could be interesting for you if:. You are working in a bioinformatics facility and you are overwhelmed with u...

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MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data. Whom is it for? MiModD was designed specifically to enable biologists/geneticists with limited bioinformatical knowledge to analyze genome-wide sequencing data of their preferred organism on off-the-shelf desktop computers. MiModD could be interesting for you if:. You are working in a bioinformatics facility and you are overwhelmed with u...

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MiModD User Guide — MiModD 0.1.7.3 documentation | mimodd.readthedocs.io Reviews

https://mimodd.readthedocs.io

MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data. Whom is it for? MiModD was designed specifically to enable biologists/geneticists with limited bioinformatical knowledge to analyze genome-wide sequencing data of their preferred organism on off-the-shelf desktop computers. MiModD could be interesting for you if:. You are working in a bioinformatics facility and you are overwhelmed with u...

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MiModD User Guide: Table of Contents — MiModD 0.1.7.3 documentation

http://mimodd.readthedocs.io/en/latest/toc.html

Platform-specific bundles of MiModD and Galaxy. Instructions for OS X (10.9 - 10.11). Instructions for Linux and other platforms. Configuring MiModD for your system. Configuration through an environment variable. Galaxy Installation and Initial Configuration. Installing and Configuring SnpEff. Installation of R and rpy2. Installation of Required Software. Installing MiModD - Examples. First steps: single-sample analysis. Multi-sample analysis: three-sample analysis of yeast mutants and their parent strain.

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MiModD User Guide: Mapping-by-Sequencing — MiModD 0.1.7.3 documentation

http://mimodd.readthedocs.io/en/latest/nacreousmap.html

The classical approach to identifying the. Mutation underlying any particular mutant phenotype consists of two separate steps:. First, genetic mapping is used to narrow down the genomic region that the mutation resides in. This is done by introducing defined genetic markers through crossing to a mapping strain and looking for linked inheritance with the mutant phenotype. Candidate DNA stretches in that region are then sequenced to identify the mutation. To be useful for mapping-by-sequencing experiments,...

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MiModD User Guide: Installation Instructions — MiModD 0.1.7.3 documentation

http://mimodd.readthedocs.io/en/latest/INSTALL.html

MiModD runs under Linux and Mac OS X (10.9 - 10.11). Software requirements are listed separately for the different installation schemes below. Hardware recommendations can be found. This is the recommended and fastest way of installing MiModD. With all requirements in place, just run:. Python3 -m pip install MiModD - user -v. To install the MiModD command line tool suite for the current user [1]. For system-wide and other installation modes. Platform-specific bundles of MiModD and Galaxy. If you prefer a...

4

MiModD Hardware Requirements — MiModD 0.1.7.3 documentation

http://mimodd.readthedocs.io/en/latest/hardware.html

In general, MiModD enables the analysis of WGS data from a wide range of model organisms on standard personal computers. Still, of course, the performance of the package will be influenced by your exact system configuration. Obvious factors to consider are:. Not only is WGS data analysis a computationally expensive task, but MiModD also tries to parallelize several steps in the analysis workflow, so a modern multi-core processor possibly supporting hyper-threading is a good choice. Or, more precisely, on...

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MiModD User Guide: The Tutorial Section — MiModD 0.1.7.3 documentation

http://mimodd.readthedocs.io/en/latest/tutorial.html

This section demonstrates the usage of MiModD by re-analysis of a number of published WGS datasets from different organisms. We will explain in detail the individual steps of each analysis and, following these steps, you will get to know much of the functionality of MiModD. All datasets used in this section are available as additional files from the MiModD download site. To set your current working directory to the directory that you want to extract the example data into, then:. Rarr; First steps: single...

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MiModD User Guide — MiModD 0.1.7.3 documentation

MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data. Whom is it for? MiModD was designed specifically to enable biologists/geneticists with limited bioinformatical knowledge to analyze genome-wide sequencing data of their preferred organism on off-the-shelf desktop computers. MiModD could be interesting for you if:. You are working in a bioinformatics facility and you are overwhelmed with u...

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