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README.md

Krona container

Main tool: Krona

Code repository: https://github.com/marbl/Krona/tree/master/KronaTools

Additional tools:

  • krona 2.8.1
  • krakentools d4a2fbe
  • pandas 2.2.3
  • biopython 1.84

Basic information on how to use this tool:

  • executables:
    • KronaTools (available as tab-completed executables):
      • ktClassifyBLAST
      • ktGetTaxInfo
      • ktImportGalaxy
      • ktImportPhymmBL
      • ktImportXML
      • ktGetContigMagnitudes
      • ktImportBLAST
      • ktImportKrona
      • ktImportRDP
      • ktGetLCA
      • ktImportDiskUsage
      • ktImportMETAREP-BLAST
      • ktImportRDPComparison
      • ktGetLibPath
      • ktImportEC
      • ktImportMETAREP-EC
      • ktImportTaxonomy
      • ktGetTaxIDFromAcc
      • ktImportFCP
      • ktImportMGRAST
      • ktImportText
    • KrakenTools (within the /KrakenTools directory):
      • combine_kreports.py
      • combine_mpa.py
      • extract_kraken_reads.py
      • filter_bracken.out.py
      • fix_unmapped.py
      • kreport2krona.py (of special interest to this image)
      • kreport2mpa.py
      • make_kreport.py
      • make_ktaxonomy.py
      • DiversityTools/alpha_diversity.py
      • DiversityTools/beta_diversity.py
  • help: provide the tool name without any arguments to see the help message (<toolname>)
  • version: Versioning information is available within the help message and can be retrieved with the following grep command <toolname> | grep "KronaTools" | cut -d' ' -f3
  • description: "Krona allows hierarchical data to be explored with zooming, multi-layered pie charts... The interactive charts are self-contained and can be viewed with any modern web browser."

Additional information: This container also contains KrakenTools, which provides a way for Krona plots to be generated for viral data.

Full documentation: https://github.com/marbl/Krona

Example Usage

# run Krona without preprocessing of the kraken output by Krakentools -- viral data will be considered "other root" but bacterial data will be visualized
ktImportTaxonomy MYSAMPLE.kraken_output_report -o MYSAMPLE.krona.hmtl -tax taxonomy

# run Krona with preprocessing of the kraken output by KrakenTools in order to visualize viral data properly
python3 /KrakenTools/kreport2krona.py -r MYSAMPLE.kraken_output_report -o MYSAMPLE.krona 
ktImportText MYSAMPLE.krona -o MYSAMPLE.krona.html