DOKK / manpages / debian 11 / radiant / ktImportPhymmBL.1.en
KTIMPORTPHYMMBL(1) User Commands KTIMPORTPHYMMBL(1)

ktImportPhymmBL - explore hierarchical metagenomic data with zoomable pie charts

Creates a Krona chart of Phymm or PhymmBL results. Note: Since confidence scores are not given for species/subspecies classifications, they inheret confidence scores from genus classifications.

ktImportPhymmBL \

[options] \ phymmbl_results_1[:magnitudes_1][,name_1] \ [phymmbl_results_2[:magnitudes_2][,name_2]] \ ...
PhymmBL results files (results.03.*). Results can also be from Phymm alone (results.01.*), but [-p] must be specified. By default, separate datasets will be created for each input (see [-c]).
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.
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: 'phymm(bl).krona.html']
[-n <string>]
Name of the highest level. [Default: 'all']
[-m <number>]
Minimum confidence. Each query sequence will only be added to taxa that were predicted with a confidence score of at least this value.
[-c]
Combine data from each file, rather than creating separate datasets within the chart.
[-d <integer>]
Maximum depth of wedges to include in the chart.
[-x <integer>]
Hue (0-360) for "bad" scores. [Default: '0']
[-y <integer>]
Hue (0-360) for "good" scores. [Default: '120']
[-p]
Input is phymm only (no confidence scores).
[-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.
August 2020 ktImportPhymmBL 2.7.1