Krona / Updates: Recent posts

GitHub

Krona is now on GitHub, beginning with KronaTools 2.6. New releases can be found at https://github.com/marbl/Krona/releases.

Posted by Brian Ondov 2015-08-25

KronaTools 2.5

  • New features
    • Standalone charts - Krona charts can now be created (using -a) that include all Krona resources and require neither an internet connection or a local KronaTools installation to be viewed
    • Unassigned improvements - Unassigned counts will now be shown even without query IDs, and magnitudes of unassigned wedges will be displayed if magnitudes are being used.
  • Fixes
    • ktImportTaxonomy will set invalid taxonomy IDs to root and produce a warning, rather than erroneously assigning them to "No hits".
    • ktImportBLAST will warn about GIs with missing or invalid taxonomy IDs, rather than running forever.
Posted by Brian Ondov 2015-03-20

KronaTools 2.4

  • New features
    • BLAST bit scores - For large query sequences, BLAST can erroneously report e-values of 0 due to floating point underflow. This can render the e-value factor (-e) ineffective when computing the lowest common ancestor, causing classifications to be too generic. Bit scores are now used instead by default, with -t specifying the range for ties. The -e option is still available and may be useful for concatenations of BLAST output against various DBs, since e-values account for DB size.
  • Fixes
    • The install script (install.pl) now works with Perl 5.14+.
Posted by Brian Ondov 2013-08-12

KronaTools 2.3

  • New features
    • Query ID Posting - Charts can now be made that can send query IDs to an arbitrary CGI script via POST. This could be used, for example, to return fasta sequences (or other information) for the queries in a given taxon. To use this feature, a web server must be running with a CGI script that can accept the queries via POST and provide an appropriate response. The url of the CGI script (including any additional variables to pass via GET) can be specified with the -qp option in any importer that uses query IDs.
    • "No rank" taxa - For data that uses NCBI taxonomy, taxa with a rank of "no rank" can now be shown with the -k option (previously these taxa were always collapsed). The taxonomy database has to be rebuilt with updateTaxonomy.sh before this option can be used.
  • Fixes
    • RDP import
      • ktImportRDP now accepts the current format of the RDP Classifier web portal output (in addition to older formats).
      • Previously, ktImportRDP could cause incorrect rank information to be shown when importing "allrank" results from the web portal (rather than "fixrank"). Rank information will now be omitted when loading "allrank".
Posted by Brian Ondov 2013-02-18

Krona viewer updates

  • The size of the chart can now be changed with buttons in the top-left corner. This makes it easier to fit long names in the window for browsing and taking snapshots.
  • The "n more" labels on hidden groups no longer include children with 0 magnitude (these occur when the children are present in another dataset, but not the current one). These children will still be labeled when zooming in, but the labels will be grayed out to distinguish them from children that are present in the current dataset.
Posted by Brian Ondov 2012-09-14

KronaTools 2.2

KronaTools 2.2
  • New features
    • ktGetTaxIDFromGI was added to translate GIs to taxonomy IDs.
    • All import scripts (except XML) now support the -n option for specifying the name of the highest level.
  • Fixes
    • RDP web portal import is fixed.
    • Occasional glitches in RDP Comparison charts caused by missing magnitudes in input files are fixed.
Posted by Brian Ondov 2012-07-12

KronaTools 2.1

  • Fixes
    • Charts can now show query IDs in Internet Explorer.
    • Charts with large numbers of query IDs (more than 10,000 in a dataset or 100,000 total) now store them in supplemental files. This improves chart performance and fixes problems with charts not loading or not displaying large numbers of queryIDs. The charts still function normally if they are moved or copied without these files, but they will not have links to query IDs.
    • Charts made with a relative url (using -u) now display in Firefox.... read more
Posted by Brian Ondov 2012-04-02

KronaTools 2.0

  • Krona 2.0
    • Charts made with KronaTools 2.0 use version 2.0 of the Krona viewer.
  • New features
    • Query IDs - For import scripts that import files with query IDs, charts can now show all query IDs assigned to a wedge and its children as well as query IDs that were assigned directly to a wedge.
    • Depth - Most import scripts now have an option (-d) to restrict the hierarchical depth that is shown in the chart.
    • Hue - Import scripts that can color the chart by score now have options (-x and -y) for specifying a custom hue range instead of the default red-green gradient.
  • New import formats
    • Enzyme Commission (EC)
      • ktImportMETAREP-EC was added to create a profile of EC numbers in METAREP
        annotations.
      • ktImportEC was added to import tabular files containing EC numbers and, optionally, query IDs, magnitudes, and scores.
    • FCP can now be imported with ktImportFCP.
    • ktImportDiskUsage can be used to show file and folder sizes.
    • GAAS output can now be imported with ktImportTaxonomy using column options.
  • Changes
    • BLAST classification (ktClassifyBLAST and ktImportBLAST):
      • ktClassifyBLAST now reports classifications for each query, rather than summarizing by taxonomy ID. Summarized results can still be obtained using -s, but the output format has changed to: magnitude, taxID, score. Also, output files now begin with a comment line that lists the fields.
      • Average log e-values reported are now log base 10 instead of log base e.
      • "Best" hits are determined by an e-value factor rather than a bit score radius.
      • Average score calculations now include all 'best' hits (hits within the
        e-value factor) for each query, rather than just the hit with the lowest e-value.
    • ktImportTaxonomy
      • Column numbers can now be specified for taxIDs, queryIDs, scores, and magnitudes.
      • Magnitude files can now be used if a column number is specified for queryIDs.
      • The default columns have changed to match ktClassifyBLAST's new default output (queryID, taxID, score).
    • ktImportMETAREP is now ktImportMETAREP-BLAST.
Posted by Brian Ondov 2012-04-02

Krona 2.0

Charts must be created with KronaTools 2.0 or later to have these changes. Older charts will continue to work, but will not receive updates.

  • New XML format
  • List attributes
    • Krona now supports attributes that are lists of values. The values can be shown for the current wedge only or for the current wedge and all of its children. This is used by KronaTools to store query IDs whenever possible.
  • Special characters
    • Special characters (including spaces, commas and quotes) in attributes no longer cause problems for Krona charts. This is due to the use of XML tags in place of XML attributes.
Posted by Brian Ondov 2012-04-02

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