Table of Contents

• Installation Instructions for MiModD and Additional Software
  • Standard Installation
    • Overview
    • Detailed Instructions
  • Galaxy Toolshed Installation
  • Platform-specific distributions
  • Configuring MiModD for your system
    • The config tool
    • Configuration through an environment variable
    • Configuration parameters
  • Running MiModD
  • Extending MiModD
    • Galaxy Installation and Initial Configuration
    • Installing and Configuring SnpEff
    • Installation of R and rpy2
  • Keeping MiModD updated
  • Package requirements
    • MiModD Hardware Requirements
    • Installation of Required Software
    • Installing MiModD - Examples
• Tutorial Section
  • Downloading example data
  • The example analyses
    • First steps: single-sample analysis
    • Multi-sample analysis: three-sample analysis of yeast mutants and their parent strain
    • Incorporating mapping-by-sequencing strategies: identification of a phenotype-causing mutation in a nematode genome
• Tool Documentation
  • Overview of the MiModD tools
    • The command line interface to the analysis tools
    • The Galaxy tool interface
    • The MiModD administrative tools
    • In-development tools
  • The MiModD tools in detail
    • The Format Converter and Query Tools
    • The Core Tools
    • The Data Exploration Tools
    • The Administrative Tools
    • In-development Tools
• 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
    • Parallel processing built into MiModD
    • Parallel execution of several MiModD tools
  • Change the order of the samples in a multi-sample vcf file
  • Import large files into Galaxy
    • Step 1: Create a Data Library to share between users
    • Step 2: Adding datasets by uploading data from a directory of files
    • Step 3: Importing library items to a history
    • Working with a linked library
  • Use gzipped fastq files in Galaxy
• MiModD and Galaxy
  • Native support of Galaxy
  • Description of MiModD workflows for GALAXY
  • Usage suggestions for MiModD from GALAXY
• Beyond MiModD: Things the package cannot do for you
  • Sequenced reads quality control
  • Indel realignment
  • Alignment visualization
• Mapping-by-Sequencing with MiModD
  • What is mapping-by-sequencing
  • What is CloudMap ?
  • MiModD complements CloudMap
  • An interface between MiModD and CloudMap
  • Analyzing whole-genome sequencing data from mapping experiments
    • Simple Variant Density (SVD) Mapping
    • Variant Allele Frequency (VAF) Mapping
• File Formats used by MiModD
  • FASTA
  • sam
  • bam
  • vcf
  • bcf
  • CloudMap-style sequence dictionary

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