Sample-level workflow for detecting Norovirus in paired-end sequencing reads using Kraken2 and estimating Norovirus GII VP1 genotype proportions through competitive BWA-MEM2 mapping. The workflow performs FastQC, Trimmomatic read trimming, Kraken2 taxonomic screening, conditional competitive VP1 mapping, reference-level coverage assessment, genotype filtering, and reporting of genotype proportions and mapping quality metrics.
This is a companion discussion topic for the original entry at github.com/adiama0/norovirus/Norovirus_GII_Competitive_Mapping