Tutorial Section

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.

Downloading example data

All datasets used in this section are available as additional files from the MiModD download site.

The dataset downloads for each example are packed as .tar.gz archives, which you need to unpack after downloading either with a graphical download manager or, through the command line, by running:

cd <path/to/unpack_directory>

to set your current working directory to the directory that you want to extract the example data into, then:

tar -xzf <path/to/downloaded_archive>

to extract the data from the downloaded archive.

The example analyses

This tutorial comprises three example analyses for three different model organisms. The analyses workflows are increasing in complexity from example to example, so if you are an absolute beginner in WGS analysis, we recommend you to go through them one by one. Users with a bit of background, on the other hand, may jump to the example that looks most interesting to them directly.

Here is the list of the example analyses:

• First steps: single-sample analysis of a cyanobacteria strain
• Multi-sample analysis: three-sample analysis of yeast mutants and their parent strain
• Mapping-by-sequencing: identification of a phenotype-causing mutation in a nematode genome