zainebhamzaoui/H3N2_variantK_Tunisia

Scripts for Tunisian A/H3N2 variant K HA analysis # Tunisian A/H3N2 variant K HA analysis This repository contains custom scripts used to analyze Tunisian A/H3N2 variant K haemagglutinin (HA) sequences collected during the 2025/2026 influenza season and to compare them with contemporaneous global HA sequences. The scripts were used for: - HA sequence processing and Nextclade analysis - extraction of HA amino-acid substitutions - generation of HA substitution lollipop plots - identification of closest international HA genetic neighbors - regional comparison of HA substitution frequencies - antigenic annotation of main HA substitutions - generation of supplementary tables ## Repository structure ```text github_H3N2_variantK_Tunisia/ ├── README.md ├── data_example/ │ └── README_data.md ├── environment/ │ └── requirements.txt ├── results_example/ ├── scripts/ │ ├── 01_run_nextclade_HA.sh │ ├── 02_extract_HA_substitutions.py │ ├── 03_generate_lollipop_HA.py │ ├── 04_closest_HA_neighbors.py │ ├── 05_regional_frequency_differences.py │ ├── 06_antigenic_annotation.py │ └── 07_generate_supplementary_tables.py └── supplementary_tables/ ├── Supplementary_Table_S1_complete_HA_substitutions.csv ├── Supplementary_Table_S2_closest_international_HA_neighbors.csv ├── Supplementary_Table_S3_Tunisian_HA_sequence_metadata.csv └── Supplementary_Tables_S1_S2_S3.xlsx