Usage

Note

Test data for most modules can be found here from a Gdrive location

Modules

• Pavian
  • Parameters
  • Returns
• NCBI Scrubber
  • Parameters
  • Returns
• Mytax
  • Parameters
  • Returns
  • WIP Procedures
  • Display
• Mytax version 2 (Metagenomics)
  • Parameters
  • Returns
  • Display
• Basestack Consensus
  • Parameters
  • Returns
    • Running Consensus Generation and Reporting
      • Starting a Run
      • Starting the process
      • Checking Logs and Status
      • Final Report
• Nextstrain
• IGV
• GAMMA
  • Parameters
  • Returns
• Rampart
  • Parameters
  • Returns
• FastQC
  • Parameters
  • Returns
• NanoPlot
  • Parameters
  • Returns
• Viral Recon
  • Parameters
  • Returns
• Bamstats
  • Parameters
  • Returns
• Artic Field Bioinformatics
  • Medaka
    • Parameters
    • Returns
  • Nanopolish
    • Parameters
    • Returns
• IVAR
  • Parameters
  • Returns
• Minimap2
  • Parameters
  • Returns
• Pangolin
  • Parameters
  • Returns
• MASH
  • Parameters
  • Returns
• VADR
  • Parameters
  • Returns
• Samtools (Under Construction)
• Unicycler
  • Unicycler Long Reads
    • Parameters
    • Returns
  • Unicycler Short Reads
    • Parameters
    • Returns
• TaxTriage (Metagenomics) (Under Construction)
  • Parameters
  • Returns

Supplemental

• Guppy Minknow
  • MinKNOW
    • Running the app
    • Testing Guppy Basecaller from MinKNOW
    • Oxford Community Forums
    • Viewing downloads
    • Setting Up Guppy for GPU
  • CUDA
  • Barcoding Kits Missing
  • Guppy GPU Basecaller
  • Reduce Runners if GPU basecalling fails
  • Running Command-line GPU Basecalling
  • Reinstalling MinKNOW
• Supplemental
• NVIDIA Jetson Setup
• Special Mentions