NAME¶

ktImportBLAST - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart of taxonomic classifications computed from tabular BLAST results.

ktImportBLAST \

[options] \ blast_output_1[:magnitudes_1][,name_1] \ [blast_output_2[:magnitudes_2][,name_2]] \ ...

blast_output

File containing BLAST results in tabular format ("Hit table (text)" when downloading from NCBI). If running BLAST locally, subject IDs in the local database must contain accession numbers, either bare or in the fourth field of the pipe-separated ("gi|12345|xx|ABC123.1|") format. 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: 'blast.krona.html']

[-n <string>]

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

[-t <number>]

Threshold for bit score differences when determining "best" hits. Hits with scores that are within this distance of the highest score will be included when computing the lowest common ancestor (or picking randomly if -r is specified). [Default: '3']

[-i]

Include a wedge for queries with no hits.

[-f]

If any best hits have unknown accessions, force classification to root instead of ignoring them.

[-r]

Pick from the best hits randomly instead of finding the lowest common ancestor.

[-p]

Use percent identity for average scores instead of log[10] e-value.

[-b]

Use bit score for average scores instead of log[10] e-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.

[-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']

[-e <number>]

E-value factor for determining "best" hits. A bit score difference threshold (-t) is recommended instead to avoid comparing e-values that BLAST reports as 0 due to floating point underflow. However, an e-value factor should be used if the input is a concatination of BLASTs against different databases.