End to end workflow for CV-A24v: trimming, de novo assembly, reference mapping with masked consensus, MAFFT alignment, IQ-TREE phylogenies for whole genome and VP1, and amino acid comparison against D90457.1. Includes scripts to fetch context genomes and optional region slicing for recombination checks.
bioinformatics snakemake next-generation-sequencing metagenomics phylogenetics public-health ahc pathogen-genomics outbreak enterovirus cva24v acute-hemorrhagic-conjunctivitis
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Updated
Jun 1, 2026 - Python