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']