Metagenomic Pipeline

This section detailed information about example pipelines made using the framework

• Tutorial
  • Initial setup
  • Getting Sequence Data
    • Taxonomy Data
  • Metagenome Assembly
  • Gene Prediction
    • Using BLAST
    • Using RAPSearch
  • Create the GFF
    • Taxonomic Refinement
    • Complete GFF
  • Alignment
  • Coverage and SNP Info
  • SNP Calling
    • bcftools
  • Data Preparation
    • Diversity Analysis
    • Count Data
    • Additional Downloads
  • Full Bash Script
• Tutorial - Exploring the Data
  • Imports
  • Download Complete Data
  • Read Necessary Data
  • Explore Count Data
    • Load Taxa Table
    • Plots for Top40 Taxa
    • Functional Categories
    • Enzyme Classification
  • Explore Diversity
    • Taxa
    • Functional Categories
    • Enzyme Classification
• Profile a Community with BLAST
  • Considerations
  • Requirements
    • MacOS X
  • Download Data
    • Assembly
    • NCBI nt
    • ID to Taxonomy
    • NCBI Taxonomy
  • Community Profiling
    • BLAST
    • Convert into a GFF
    • Adding the Taxonomic Information
    • Filter the GFF
    • Getting the Profile
• Gene Prediction
  • Prediction Software
  • General Procedure
  • Functional Prediction
    • Generate Profiles
  • Filter Annotations
  • Taxonomic Prediction
    • Last Common Ancestor
  • Complete Annotations
  • Examples
    • Gene Prediction with BLAST+