Welcome to KvarQ’s documentation!

Contents

• Installing KvarQ
  • Precompiled packages
  • Installing KvarQ From Source
• Using KvarQ Command Line Interface (CLI)
  • Using The Command Line
  • Loading of Testsuites
  • Scanning a File
  • Extracting results from a batch of scans
  • Showing information about testsuites
  • Directly Analysing a .fastq
  • Showing Results
  • Updating Results
  • More Usage Examples
• Using KvarQ Graphical User Interface (GUI)
  • Launching the GUI
  • Configuring KvarQ
  • The Scanner
  • The Explorer
• KvarQ testsuites
  • Rolling your own testsuite
  • Versions, Compatibility
  • Annotated example
• Tutorial
  • Ebola Outbreak 2014
  • Creating a new SNP testsuite
• Understanding the Scanning Process
  • Overview
  • Configuration Parameters
• Hacking KvarQ
  • About flanks
  • About positions
  • About the complementary DNA strand
  • Sequence of tests
  • About clonal variants (“heterozygous calls”)
• Glossary
• How to cite
• Changelog
  • version 0.12.2
  • version 0.12.1
  • version 0.11.3
  • version 0.11.2
  • version 0.11.1
  • version 0.10.10
  • version 0.10.9
  • version 0.10.8
  • version 0.10.7
  • version 0.10.6
  • version 0.10.5