Inhalt

•  
  Introduction
•  
   Preface
•  
   Structure of this document
•  
  Background
•  
   Microbial community analysis
•  
   Metataxonomics
•  
   Metagenomics
•  
   Metatranscriptomics
•  
   Sequencing technologies
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   Low-throughput sequencing
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   Next-generation sequencing
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   Third generation sequencing
•  
   Bioinformatics tools for the analysis of microbial community data
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   BLAST and derived methods (LCA, SOrt-ITEMS, CARMA3)
•  
   Accelerated sequence homology search
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   HMMER
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   RDP Classifier
•  
   MetaPhlAn
•  
   Kraken
•  
   Kraken 2
•  
   Kaiju
•  
   Centrifuge
•  
   Metagenome analysis platforms
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   MG-RAST
•  
   IMG/M
•  
   EBI MGnify
•  
   CyVerse
•  
   MEGAN
•  
   Preliminary conclusions
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   MGX: An advanced framework for microbial community analysis
•  
   Objectives
•  
   System architecture
•  
   The importance of metadata
•  
   Server
•  
   Data model and sequence storage
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   Workflow-based analysis
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   Data serialization
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   Security and access control
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   MGX client library
•  
   Graphical user interface
•  
   Project Structure
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   Data Import
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   Quality Control
•  
   Job Execution
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   Visualization and Reporting
•  
   Sequence Export
•  
   Search
•  
   Statistical data interpretation
•  
   Reference mapping
•  
   Fidelity assessment of workflows
•  
   Currently available pipelines
•  
   Evaluation and benchmarking of taxonomic classification approaches for environmental DNA sequences
•  
   Taxonomic classification approaches
•  
   MGX classification workflow
•  
   Generation of benchmark datasets
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   Performance evaluation
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   Conclusion
•  
   Sequence alignment evaluation
•  
   Runtime measurement
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   Accuracy evaluation
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   Refinement of the taxonomic classification workflow
•  
  Discussion and Outlook
•  
   Discussion
•  
   Completed studies
•  
   Outlook
•  
   Preprocessing and quality control
•  
   Metagenome assembly
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   Selection of data processing engine
•  
   Containerization of MGX components
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   Standardized functional analysis
•  
   Public metagenome resource
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  Conclusion
•  
   Appendix
•  
   Implementation of custom analysis pipelines
•  
   Setting up the Conveyor workflow Designer
•  
   Basic workflow requirements
•  
  Annotating metagenome sequences
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   Performing basic sequence annotation
•  
   Annotation of hierarchical attributes
•  
   Workflow import into MGX
•  
   MGX database model
•  
   Bibliography