centrifuge-summary

Summarise a Centrifuge report for a specific taxon and its sub-taxa

Dependencies

taxonkit

Usage

centrifuge-summary --taxon-name "Escherichia coli" --report-file example.centrifuge.report.tab

also works for other taxonomic levels:

centrifuge-summary --taxon-name "Enterobacteriaceae" --report-file example.centrifuge.report.tab

and NCBI taxon IDs:

centrifuge-summary --taxon-id 561 --report-file example.centrifuge.report.tab

Report uniquely matching reads (default if neither -u or -a are supplied):

centrifuge-summary -u --taxon-id 561 --report-file example.centrifuge.report.tab

or reads that match at least the target taxon:

centrifuge-summary -a --taxon-id 561 --report-file example.centrifuge.report.tab

Help

usage: centrifuge-summary [-h] (-t TAXONNAME | -i TAXID) [-u | -a] -r
                          REPORTFILE

optional arguments:
  -h, --help            show this help message and exit
  -t TAXONNAME, --taxon-name TAXONNAME
                        Scientific name of the taxon to count reads beneath
                        [e.g. Escherichia]
  -i TAXID, --taxon-id TAXID
                        NCBI taxID to count reads beneath [e.g. 561]
  -u, --unique          Summarize only reads UNIQUELY matching taxon
                        [numUniqueReads column] [DEFAULT]
  -a, --all             Summarize reads matching taxon [numReads column]
  -r REPORTFILE, --report-file REPORTFILE
                        Path to the centrifuge report-file to summarise