NAME¶

ktImportFCP - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart based on the results of FCP (Fragment Classification Package).

ktImportFCP \

[options] \ fcp_output_1[:magnitudes_1][,name_1] \ [fcp_output_2[:magnitudes_2][,name_2]] \ ...

fcp_output

Results of running any FCP classification tool (except BLASTN.py, which only outputs raw BLAST results). 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: 'fcp.krona.html']

[-n <string>]

Name of the highest level. [Default: 'root']

[-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.

[-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.