Welcome to MetaDIVE's documentation!

MetaDIVE is a metagenomics analysis pipeline which specialises in the high accuracy and low false negative detection. of both known and highly novel viruses. MetaDIVE can be run in several ways depending on the modules chosen and the key goals of your project.

• MetaDIVE Overview
  • Core Module (Module 1): Data filtering, assembly, and viral classification
  • Module 2: Microbiome Classification
  • Module 3: Dynamic Host Identification and Depletion
  • Module 4: Single Reads Analysis
  • Module 5: Diverged read/contig detection
  • Module 6: Adaptive Viral Reference Mapping
  • Module 7: Adaptive Viral Tree Building
  • Module 8: Adaptive Viral Contig Clustering

• Installation guide
  • Conda Installation
  • Downloading MetaDIVE
  • Building MetaDIVE scripts
  • MetaDIVE environments
  • MetaDIVE databases
• Run setup
  • pipeline folder
  • config file
    • Samples to run
    • Working program directory
    • Run memory requirements
    • Core module program specific settings
    • Module settings
    • Database paths
  • Running MetaDIVE
  • Rerunning MetaDIVE/running on new datasets

• Interpreting results
  • Results folders
  • Summary_results_combined_figures_and_tables_contigs
  • Summary_results_per_sample_contigs
  • raw_assemblies
  • CO1/LSU/SSU_results folders
  • combined_raw_reads_and_contigs_viruses
  • Metabat_binned_contigs
  • Reference_guided_viral_genomes

• Detailed Conda environments used
• Detailed databases information
• Detailed description of scripts files
• Detailed description of rules files
• Common issues and troubleshooting
• Software references

Note

This project is under active development