Best practices for the implementation of WGS in clinical and public health labs include the requirement for transparency, auditability and traceability of data and analyses. The methods and parameters used in WGS-based analyses can influence results and their interpretation, which can have significant implications for genomic epidemiology investigations. Such analyses generate key evidence supporting clinical and epidemiological interventions, which can have legal and medical ramifications. Therefore, it is crucial to maintain consistent, comprehensive and transparent records regarding how and when evidence was generated.

To ensure processes are carefully documented, all information regarding data provenance and analytical parameters is stored within the log files of the IRIDA database. Output files from an analysis are archived on a User’s file system and can not be deleted from IRIDA (even if a User deletes an analysis). All files used to generate analysis results are available under the Input Files tab. The Provenance tab shows information about all the steps and parameters used to generate any result listed in a tree format with the top entry representing the individual Galaxy tool used to generate the output file. Furthermore, if a User is added then later removed from a Project, there will be a time-stamped entry in the IRIDA database showing both instances and their author.

The ability to track and record parameters and processes increases auditability and transparency, and better facilitates comparisons between analyses.