Home

With this Metagenome-Simulation Pipeline you can create a simulated metagenome dataset out of a list with genomes. It uses 16S Marker gene comparison to classify these genomes and predict a novelty category to improve the generation of a simulated community. For the community design the program draws from different taxonomic ranks genomes to get a community complexity chosen by the user. Then the ART readsimulator generates paired-end reads which get anonymized.

##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
• Acknowledgments and Contact