Vaccine induced selection pressure on seasonal influenza in mice

Authors

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This repository host the scripts for analyzing the nucleotide diversity (π) via deep-sequencing data in the study "Vaccine induced selection pressure on seasonal influenza in mice". The viral population diversity measurements including πN and πS were estimated using SNPGenie.

Details:

1. ./scripts/0.resequencing.sh: The raw Illumina fastq reads were aligned to the reference using BWA-MEM2 (v2.0). Primer trimming and quality trimming were performed using iVar. Variants using for population diversity estimation were called by samtools mpileup and ivar variants.
2. ./scripts/nu_diversity.R: Building GTF, VCF and other files needed for input for SNPGenie.

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