---
name: "ktImportTaxonomy"
section: "1"
platform: "linux"
package: "radiant"
version: "2.8.1+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ktImportTaxonomy"
---

# ktImportTaxonomy(1)

explore hierarchical metagenomic data with zoomable pie charts

## NAME

ktImportTaxonomy - explore hierarchical metagenomic data with zoomable pie charts

## DESCRIPTION

-

  Creates a Krona chart based on taxonomy IDs and, optionally, magnitudes and scores. Taxonomy IDs corresponding to a rank of "no rank" in the database will be assigned to their parents to make the hierarchy less cluttered (e.g. "Cellular organisms" will be assigned to "root").

-

  ktImportTaxonomy \\

-

  \[options\] \\ taxonomy\_1\[:magnitudes\_1\]\[,name\_1\] \\ \[taxonomy\_2\[:magnitudes\_2\]\[,name\_2\]\] \\ ...

- taxonomy

  Tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes and scores. By default, query IDs, taxonomy IDs and scores will be taken from columns 1, 2 and 3, respectively (see **-q**, **-t**, **-s**, and **-m**). Lines beginning with "#" will be ignored. By default, separate datasets will be created for each input (see \[-c\]).

- magnitudes

  Optional file listing query IDs with magnitudes, separated by tabs. This can be used to account for read length or contig depth to obtain a more accurate representation of abundance. By default, query sequences without specified magnitudes will be assigned a magnitude of 1. Magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes.

- name

  A name to show in the list of datasets in the Krona chart (if multiple input files are present and \[-c\] is not specified). By default, the basename of the file will be used.

-

  - \[-o \<string\>\]

  Output file name. \[Default: 'taxonomy.krona.html'\]

- \[-n \<string\>\]

  Name of the highest level. \[Default: 'Root'\]

- \[-i\]

  Include a wedge for queries with no hits.

- \[-c\]

  Combine data from each file, rather than creating separate datasets within the chart.

- \[-q \<integer\>\]

  Column of input files to use as query ID. Required if magnitude files are specified. \[Default: '1'\]

- \[-t \<integer\>\]

  Column of input files to use as taxonomy ID. \[Default: '2'\]

- \[-s \<integer\>\]

  Column of input files to use as score. \[Default: '3'\]

- \[-m \<integer\>\]

  Column of input files to use as magnitude. If magnitude files are specified, their magnitudes will override those in this column.

- \[-d \<integer\>\]

  Maximum depth of wedges to include in the chart.

- \[-k\]

  Show the "cellular organisms" taxon (collapsed by default).

- \[-K\]

  Collapse assignments to taxa with ranks labeled "no rank" by moving up to parent.

- \[-x \<integer\>\]

  Hue (0-360) for "bad" scores. \[Default: '0'\]

- \[-y \<integer\>\]

  Hue (0-360) for "good" scores. \[Default: '120'\]

- \[-u \<string\>\]

  URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). Reduces size of charts and allows updates, though charts will not work without access to this URL.

- \[-qp \<string\>\]

  Url to send query IDs to (instead of listing them) for each wedge. The query IDs will be sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". The url can include additional variables encoded via GET.

- \[-tax \<string\>\]

  Path to directory containing a taxonomy database to use. \[Default: '/usr/share/perl5/KronaTools/taxonomy'\]