KronaTools-2.8.1

Snapshot fix

KronaTools-2.8

BLAST classification update

• Compatibility for upcoming NCBI taxonomy lookup changes (see #150)
• ktImportBLAST and ktClassifyBLAST now default to ignoring unknown accessions rather than forcing queries with hits to those accessions to root; -f (force) restores old behavior

KronaTools-2.7.1

Minor bug fixes.

Krona Excel Template v2.5

• Multiple datasets are now supported, instead of just two. This is achieved with an extra column that specifies which dataset each line should contribute to.
• Unicode characters are now supported via UTF-16 output.
• Installation has been removed. Simply open the template to begin using it.

Krona Excel Template v2.4

• The template now creates self-contained charts to avoid "could not get resources" errors.
• A second dataset can now be entered and included in the same chart.

KronaTools-2.7

Features

• Charts now take full advantage of high resolution (e.g. Retina) displays.
• updateTaxonomy.sh has been improved for installations without internet
  connectivity.
  • --local has been divided into --only-fetch and --only-build, so
    data dumps can be downloaded automatically before transferring.
  • Custom taxonomy directories can now be relative paths.
  • A new --preserve option prevents data dumps from being removed after
    building, if needed for other uses.
  • Data dumps can be unzipped/untarred.
  • Updating the taxonomy ID lookup database (now by accessions), has been
    split out to updateAccessions.sh, which cuts most of the running time from
    updateTaxonomy.sh when lookups are not needed.
• New taxonomy convenience scripts
  • ktGetTaxInfo lists depth, parent, rank, and name for taxonomy IDs, or
    can directly take accessions, if the database has been installed with
    updateAccessions.sh.
  • ktGetLCA returns the lowest common ancestor for groups of taxonomy IDs,
    or can directly take accessions, if the database has been installed with
    updateAccessions.sh.

Fixes

• ktImportKrona will no longer fail if a chart's supplemental files are not
  available.
• ktImportTaxonomy no longer erroneously creates supplemental file folders
  for large imports without query IDs.

Changes

• GI lookups have been replaced with accession lookups due to the impending
  retirement of GIs by NCBI.
  • ktGetTaxIDFromGI is now ktGetTaxIDFromAcc.
• ktGetLibPath, which caused problems with multiple KronaTools installations,
  is no longer used by official scripts, which now always use relative paths to
  find their appropriate libraries and data. The command is still available for
  third-party inclusion of the KronaTools library .
• Warnings and errors are now directed to STDERR instead of STDOUT.
• The "Unassigned" (gray) section of the current chart view is now "other"
  for clarification.

KronaTools-2.6.1

Fixes a bug in ktImportTaxonomy that would change "No hits" (taxonomy ID of 0 or -1) to root.

KronaTools-2.6

This release marks the migration from SourceForge to GitHub. For previous releases, see:
https://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/

• Standalone charts - Charts are now standalone by default. To point to a web server with Krona resources, such as the Krona GitHub, the URL of the server has to be provided with -u, e.g. -u http://marbl.github.io/Krona.
• Custom taxonomy directories - Multiple taxonomy databases can now be maintained by providing a custom directory to updateTaxonomy.sh, e.g. updateTaxonomy.sh /path/to/taxonomy/. To use a custom taxonomy directory for creating a chart, specify -tax /path/to/taxonomy/ to the import script.
• ktImportKrona - A new ktImportKrona command creates Krona charts from the data in other Krona charts. This allows consolidation of compatible charts into multi-charts, as well as conversion to standalone charts and other minor chart tweaks.