Importing from supported tools

NOTE: For script usage information, any script can be run without parameters.

RDP

• Taxonomic classifications of the Ribosomal Database Project 16S Classifier can be imported using ktImportRDP. To download classifications:
  1. Run the classification tool.
  • Click "show assignment detail" for the root of the hierarchy.
  • Click "download allrank result" or "download fixrank result".
• Comparisons from the RDP Library Compare tool can be imported using ktImportRDPComparison. To download comparison results:
  1. Run the comparison tool.
  2. Click "download comparison result as text".

PhymmBL

• A taxonomical profile of PhymmBL classifications can be created using ktImportPhymmBL.
• Example:
  • ktImportPhymmBL phymmbl/results.03.*

BLAST

• A taxonomic profile of BLAST results can be created with ktImportBLAST. Results must in tabular format (use "Hit table [text]" when downloading results from NCBI). GI numbers from the top hits are used to obtain NCBI taxonomy IDs, which are used to create a tree. Ties for top hits can be broken by going up to the lowest common ancestor (default) or by picking one at random. The Krona Tools installation must have local taxonomy information installed using updateTaxonomy.sh (see [Installing]).

MG-RAST

• Taxonomic or functional classifications can be imported from the MG-RAST metagenomics server using ktImportMG-RAST.
• Downloading data from MG-RAST:
  1. From the home page, click Browse Metagenomes.
  • Select a project, then select a metagenome from that project (e.g. 4441138.3).
  • Click on the small bar chart icon to analyze the metagenome.
  • Under Analysis Views, choose Hierarchical Classification (organism or functional) or Lowest Common Ancestor.
  • Select "table" under Data Visualization and click the "generate" button .
  • Adjust the table options as desired and click "download data matching current filter".

METAREP

• A taxonomical profile of a METAREP data set can be created with ktImportMETAREP. NCBI taxonomy IDs from the top hits in the blast.tab file of the data set are used to create a tree. Query lengths are use for magnitudes. Ties for top hits can be broken by going up to the lowest common ancestor (default) or by picking one at random. The Krona Tools installation must have local taxonomy information installed using updateTaxonomy.sh (see [Installing]).
• To download and import data from METAREP:
  1. From the home page, log in or choose "Try It".
  • View a project.
  • Choose "Download" for desired libraries in the project or choose "Download All Libraries" and unpack the downloaded file.
  • Unpack each library to be imported.
  • Unzip blast.tab.gz in each of the library folders to be imported.
  • Run ktImportMETAREP with the desired library folders.
    • Example:
      • ktImportMETAREP HOT01-0010M HOT02-0070M

MEGAN

• MEGAN taxonomic classifications can be imported using ktImportTaxonomy.
• To export classifications:
  1. From the menu, choose Select -> All Nodes.
  • From the menu, choose File -> Export -> CSV Format.
  • In "Choose format", choose "read-name, taxon-id".
  • In "Choose separator", choose "tab".