Pipeline logic
Pipeline steps
Read QC
Low-quality bases are trimmed from the ends of each read. After trimming, the read is discarded if fewer than 50% of its bases have a quality score greater or equal to q20, the read is shorter than 32 bp, or the read has 5 or more ambiguous bases. It is assumed that appropriate adapter trimming has already been performed.
Optional
X
X
X
X
X
X
Dehosting
Human read removal using the DRAGEN Kmer Classifier
X
X
X
X
X
X
Sample QC
Sample composition and enrichment factor calculations
Internal control required to calculate the enrichment factor
X
X
X
Microorganism classification
Pre-alignment filtering step
Configurable sensitivity
X
X
X
Microorganism detection
Reference alignment, consensus sequence generation, variant calling
X
X
X
X
X
X
Microorganism quantification
Absolute copies/mL calculation
Quantitative internal control and concentration required
X
X
X
Microorganism reporting thresholds
Proprietary algorithms or user-defined reporting logic
X
X
X
X
X
Bacterial AMR marker analysis
Nucleotide and protein alignment, consensus sequence generation, variant calling and annotation
X
X
Viral AMR marker analysis
Variant calling and annotation
X
X
X
X
Viral clade and lineage prediction
Pangolin, Nextclade
X
X
X
X
Result filters
User-specified filters applied
X
X
X
X
X
Reporting - Analysis level
XLSX, HTML, ZIP
X
X
X
X
X
X
Reporting - Sample level
JSON, HTML, FASTA (consensus sequences), VCF (viral variants)
X
X
X
X
X
X
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