NAME

       ktClassifyBLAST - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION

       Assigns each query in tabular BLAST results to an NCBI taxonomy ID. If the results contain
       comment lines, queries with no hits will be included in the output (with taxonomy  IDs  of
       -1 for consistency with MEGAN).

       ktClassifyBLAST \

              [options] \ blast_output_1 \ [blast_output_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.

       [-o <string>] Output file name. [Default: 'blast.taxonomy.tab']

       [-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']

       [-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.

       [-s]   Summarize counts and average scores by taxonomy ID.

       [-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.

       Default:          <queryID> <taxID> <score>

       Summarized (-s):  <count> <taxID> <score>

       queryID
              The query ID as it appears in the BLAST results.

       taxID  The NCBI taxonomy ID the query was assigned to (or -1 if it has no hits).

       score  The score of the assignment(s); by default, the average E-value of "best" hits (see
              -p, -b).

       count  The number of assignments.