📂Output file summary
Note: Some files may not be generated depending on user inputs and pipeline outcome
Summary table of output files
| Filename | Type | Description |
|---|---|---|
viral_consensus_genomes | Dataset | Directory containing single sample consensus genome(s) that were generated. Each fasta file within the directory contains a single viral genome. There is a Dataset for each sample with results |
Samplename.Panelname.report.html | html | Report visualization for a single sample: includes Sample Quality Control, Microorganisms present, Antimicrobial Resistance Markers (only for Influenza and bacteria/fungi) and User Options, separated by tabs |
Samplename.Panelname.report.json | json | See JSON report section for information on file contents |
Samplename.Panelname.viral_genomes_consensus.fa | fasta | Full-genome consensus sequence(s) for all viruses reported in the sample (nucleotide sequences) |
Samplename.Panelname.viral_targets_consensus.fa | fasta | Consensus sequence(s) for each targeted gene for all viruses reported in the sample (nucleotide sequences) |
Samplename.Panelname.bacterial_amr_nucleotide_consensus.fa | fasta | Consensus sequence(s) for all bacterial AMR markers reported in the sample (nucleotide sequences) |
Samplename.Panelname.bacterial_amr_protein_consensus.fa | fasta | Consensus sequence(s) for all bacterial AMR markers reported in the sample (amino acid sequences) |
Samplename.Panelname.viral_variants.vcf | vcf | Variant call file with viral consensus genome and closest matching reference genome |
Analysis Results | Dataset | Directory with three files including: Excel results for all samples, zip file with all files available for download, and html report with summary of all samples |
AnalysisIDnumber.Panelname.report.xlsx | Excel compatible file | Sample, Microorganism, AMR, and Variant results from all samples in the analysis. Further details on the fields in the Sample Report are included below the table. |
AnalysisIDnumber.Panelname.results.zip | Zip | Compressed Zip file containing all of the result files available for download |
report.html | html | Report visualization including Summary of all Sample Composition (reads off target/on target, Unclassified, Internal Controls, etc) and Summary Statistics of all samples within an analysis run |
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