Table of Contents

Welcome and Overview page

Installation Guide

• MiModD Hardware Requirements

• Choosing an installation type
  • Standard Installation
  • Galaxy Toolshed Installation
  • Preconfigured bundles of MiModD and Galaxy

• Standard Installation
  • Instructions for OS X / macOS (10.9 - 10.15)
  • Instructions for Linux and other platforms
    • MiModD Installation Examples
    • Installation of Required Software
  • Start using MiModD
  • Adding additional functionality
    • Galaxy Installation and Initial Configuration
    • Installation of R and rpy2
    • Installing and Configuring SnpEff
  • Keeping MiModD updated

• Galaxy Toolshed Installation
  • Installation
  • Configuration
  • Enhancing the user experience

• Configuring MiModD for your system
  • Configuration from the command line
  • Configuration through an environment variable
  • Configuration parameters

User Guide

• Tutorial Section
  • Downloading example data
  • 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

• Mapping-by-Sequencing with MiModD
  • What is mapping-by-sequencing?
  • Mapping-by-sequencing support in MiModD
    • Overview
    • Three types of linkage analyses in MiModD
    • Usage examples
  • MiModD for users of CloudMap

• How to - MiModD recipes
  • Overview of recipes
  • Add the mimodd executable to $PATH
  • Re-align coordinate-sorted (previously aligned) reads
  • Prepare and use a custom hyperlink template file
  • Understand and use multiprocessing efficiently
  • Change the order of the samples in a multi-sample vcf file

• MiModD and Galaxy
  • Native support of Galaxy
  • Usage suggestions for MiModD from Galaxy
  • Using MiModD on public Galaxy servers
  • Description of MiModD workflows for Galaxy

• Beyond MiModD: Things the package cannot do for you
  • Sequenced reads quality control
  • Indel realignment
  • Alignment visualization

• Tool Documentation
  • Command line help system
  • Overview of the MiModD tools
  • The MiModD tools in detail

• File Formats and Compatibility
  • Character Encoding
  • MiModD File Format Specifications

Other Topics

• Python API
  • Description of the MiModD Python modules in alphabetical order