ktClassifyBLAST - explore hierarchical metagenomic data with
zoomable pie charts
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']
- [-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.