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.