WGS of Influenza A virus:  - BL6M R10 C - HOM
Library preparation was conducted using the Illumina Nextera DNA Flex Library Prep Kit, followed by size selection and quantitation. Indexed libraries were pooled, and qRT-PCR was used to determine viral genome copy number prior to sequencing. Adapters were removed using cutadapt, and reads were aligned to the HK68 reference genome with bowtie2. Duplicates were marked and removed using Picard and samtools, and variants were called using deepSNV. Filtering criteria included a p-value < 0.05, Phred quality score >35, mapping quality (MapQ) >30, and read positions between 40 and 200. Samples with low sequencing coverage were excluded from further analysis.