Requires biopython to build optional trees.
Usage: kraken_taxonomy_report.py [options] file1 file...fileN
Options:
-h, --help show this help message and exit
-v, --version print version and exit
--show-zeros Show empty nodes
--header-line Provide a header on output
--intermediate Intermediate Ranks
--name-id Use Taxa ID instead of Name
--name-long Use Long taxa ID instead of base name
--taxonomy Output taxonomy in last column
--cluster=CLUSTER Cluster counts to specified rank
--summation Add summation of child counts to each taxa
--sanitize-names Replace special chars ( | |\||\.;) with underscore (_)
--show-rank Output column with Rank name
--db=DB Name of Kraken database
--output=OUTPUT Name of output file
--output-tree=OUTPUT_TREE
Name of output file to place newick tree