📄Microorganism Reporting File format

Enrichment panel	Template file
Illumina Respiratory Pathogen ID/AMR Enrichment Panel Kit (RPIP)	RPIP_6-5-1_Microorganism_Reporting_Template.xlsx
Illumina Urinary Pathogen ID/AMR Enrichment Panel Kit (UPIP)	UPIP_8-6-0_Microorganism_Reporting_Template.xlsx
Illumina Respiratory Virus Oligo Panel / Respiratory Virus Enrichment Kit (RVOP / RVEK)	RVOP_2-7-0_Microorganism_Reporting_Template.xlsx
Illumina Viral Surveillance Panel (VSP)	VSP_2-7-0_Microorganism_Reporting_Template.xlsx
Illumina Viral Surveillance Panel V2 (VSP V2)	VSPV2_2-7-0_Microorganism_Reporting_Template.xlsx

How to edit the template file

1. First, we recommend saving the provided template file with a new name

2. Do not add any new columns and do not delete any columns from the template file

3. Do not change or remove any text from the header row. **The "kmer_read_count" metric is only valid with the UPIP enrichment panel.

4. Rows with microorganism names that are not of interest can be deleted. However, the entire tiered reporting group for certain viruses must be included to preserve tiered reporting logic (if desired). Membership in a tiered reporting group means that a hierarchical relationship is pre-built into the database and the most granular tier level passing reporting thresholds is reported. For example, if Influenza B virus (B/Victoria/2/87-like) or Influenza B virus (B/Yamagata/16/88-like) are reported in a sample then the less granular Influenza B virus reporting name will NOT be reported. See the "Has Tiered Reporting" and "Reporting Tier" columns of the "Microorganisms" table in the Panel Summary for RPIP, RVOP/RVEK, VSP, and VSP V2 to select and see which viruses are reported as part of a tiered reporting group.

5. Upload the microorganism reporting file to a BaseSpace Project. **It is only necessary to upload the file once.

6. Select the file by clicking on the "Dataset File(s)" option under the "User-defined specification" section.

Example user-defined microorganism reporting file

See example below for 6 RPIP microorganism reporting names. Prediction logic can be specified on a microorganism-by-microorganism basis using multiple parameters and combinatorial logical expressions.

reporting_name	prediction_logic	coverage	median_depth	ani	aligned_read_count	rpkm	kmer_read_count
Acinetobacter baumannii	default
Cryptococcus neoformans	coverage	0.3
Escherichia coli	aligned_read_count				200
Human adenovirus E	(coverage AND median_depth) OR (aligned_read_count AND ani)	0.1	1	0.95	100
Human bocavirus 1 (HBoV1)	rpkm OR (ani AND coverage) OR median_depth	0.2	5	0.9		5
Klebsiella pneumoniae	default AND coverage	0.5