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With the emSEP metagenome simulation pipeline you can create different kinds of metagenome datasets (single sample, differential abundance, time series) from bacterial and archaeal genomes, including viral and plasmid data sets.

##User Manual

• Introduction
• Installation
  • Dependencies
• Usage
• Overview
  • Taxonomic annotation, OTU inference and novelty category assignment for bacterial and archaeal genomes
    1. Reference data preparation
    2. Finding and extracting marker genes
    3. Alignment and clustering
    4. Annotation
  • Metagenome simulation
    1. Data preprocessing and validation
    2. Community Design
       • Genome selection
       • Creating the community abundances
    3. Metagenome sample simulation
    4. Creation of the gold standards and anonymization
• Command line Arguments
• Configuration File Options
  • Genome annotation
  • Metagenome Simulation
• File Formats
  • Genome annotation
  • Metagenome Simulation
• References
• Acknowledgments and Contact