In-house python scripts for influenza virus sequencing using Nanopore, made available to accompany https://doi.org/MGEN-D-23-00116
This repository contains two in-house scripts, written to work within a local environment and file structure:
1) cidr_flu_consensus_pipeline.py - consensus generation, HA clade identification and NA/PA inhibitor antiviral resistance identification
2) cidr_flu_epi.py - segment alignment, concatenation, pairwise SNP comparison and ML tree generation