📄Microorganism reporting file templates

Panel	Template File
Illumina Respiratory Pathogen ID/AMR Enrichment Panel Kit (RPIP)	RPIP_6-3-0_Microorganism_Reporting_Template.xlsx
Illumina Urinary Pathogen ID/AMR Enrichment Panel Kit (UPIP)	UPIP_8-4-0_Microorganism_Reporting_Template.xlsx
Illumina Respiratory Virus Oligo Panel / Respiratory Virus Enrichment Kit (RVOP / RVEK)	RVOP_Microorganism_Reporting_Template.xlsx
Illumina Viral Surveillance Panel (VSP)	VSP_Microorganism_Reporting_Template.xlsx
Illumina Viral Surveillance Panel V2 (VSP V2)	VSPV2_2-4-0_Microorganism_Reporting_Template.xlsx

Editing this file

1. Do not delete or rename columns, and do not add additional columns.

2. To create a user-defined subset list of organisms on panel to target, do not change the prediction logic but delete rows of the unwanted microorganisms. For example, here is a reporting table of three bacteria with default report tresholds.

Reporting Name	Prediction Logic	Coverage	Median Depth	ANI	Aligned Read Count	RPKM	Kmer Read Count
Klebsiella pneumoniae	default
Cryptococcus neoformans	default
Acinetobacter baumannii	default

Note that if sub-selecting to keep Influenza or Enterovirus (including Coxsackievirus, Poliovirus, and Echovirus) this analysis may require additional support.