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.

ktImportBLAST 2.8                                   June 2021                                   KTIMPORTBLAST(1)