Welcome to Computational Boot Camp’s documentation!

Contents:

• Quality Control
  • Basic Example Workflow
  • Trimming Adapters
  • Removing Poor Quality Bases
  • Removing Replicate Reads
  • Understanding Your Read Data
  • FastQC Test Information
  • Our QC Workflow Commands and software
• Assembly
  • What is Assembly?
  • De Bruijn Graphs
  • Assembly Considerations
  • Running the software
• Mapping
  • What is Mapping?
  • How it Works
  • The Burrows-Wheeler Transform
  • Mapping to the BWT/FM index
  • What data comes from Mapping
  • Sofware for mapping outputs
• Binning (with CONCOCT and ANVIO)
  • What is Binning?
  • How does CONCOCT work
  • Deviation from defaults
  • Bin Refinement with ANVIO
  • Assessing bin quality
  • Dereplicating bins
• A Full Metagenomics Run
  • 1. Create your working directory
  • 2. Move a copy of your raw reads to your working directory
  • 3. Run QC on each set of your reads
  • 4. Assembly
  • 5. All vs All mapping for differential coverage for binning
  • 6. Binning with concoct
  • 7. Create ANVIO Databases for Manual Refinement
  • 8. Manually refine bins in anvio
  • 9. Merge and dereplicate bin sets
  • 10. Competitively map to dereplicated bins (an example of using the pipeline for other steps)
  • 11. Some extra notes
• Shared Resources
  • Conda envs
  • Databases
  • Containers
• Resources for Working on Greatlakes
• Basic Singularity usage
  • Running software in existing containers
  • To build a Container with singularity on Greatlakes

Indices and tables

• Index
• Module Index
• Search Page