Quicksand's documentation

Table of content

• Pipeline
  • Workflow
    • Filtering
    • Taxonomic classification
    • Mapping and Deduplication
    • DNA Deamination Stats
  • Fixed References
  • Rerun
    • References
• Quickstart
  • Requirements
  • Download test-data
  • Download the database
  • Run quicksand
• Configuration
  • Config-file
  • Environmental variables
  • Intermediate files
• Flags
  • Required flags
  • Optional flags
  • Profiles
• Input and Output
  • Input
  • Output
    • Files
• Filters
  • Percentage based filter
  • Breadth of coverage based filter
• Examples
  • Regular run
  • Filter the final_report
  • Fixed references
  • Rerun