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.