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tbp-parser

Not for Diagnostic Use

CAUTION: The information produced by this program should not be used for clinical reporting unless and until extensive validation has occured in your laboratory on a stable version. Otherwise, the outputs of tbp-parser are for research use only.

FUTURE DEPRECATION NOTICE

At the time of the PHB v2.3.0 release:

  • all branches on Terra that have been mentioned in this documentation will be deleted. Please use the v2.3.0 version of TheiaProk moving forward.
  • the main branch of tbp-parser will host v2.1.0 and above; earlier versions of tbp-parser will no longer be supported
  • future releases of tbp-parser will only support outputs generated by TBProfiler v6.0.0 and above.

Versions of TBProfiler prior to v6.0.0 are not compatible with v2+ of tbp-parser. Please ensure that you are using the correct version of tbp-parser for your version of TBProfiler.

Overview

tbp-parser is a tool developed in partnership with the California Department of Health (CDPH) to parse the output of Jody Phelan’s TBProfiler tool into four additional files:

  1. A Laboratorian report, which contains information about each mutation detected and its associated drug resistance profile in a CSV file.
  2. A LIMS report, formatted specifically for CDPH’s STAR LIMS, which summarizes the highest severity mutations for each antimicrobial drug and the relevant mutations.
  3. A Looker report, which condenses the information contained in the Laboratorian report into a format suitable for generating a dashboard in Google’s Looker Studio.
  4. A coverage report, which contains the percent coverage of each gene relative to the H37Rv reference genome in addition to any warnings, such as any deletions identified in the gene that might have contributed to a reduced percent coverage

Please reach out to us at support@theiagen.com if you would like any custom file formats and/or changes to these output files that suit your individual needs.