seasonal-flu

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Scripts. config, and snakefiles for seasonal-flu nextstrain builds

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최종 버전 다운로드 (.zip)

- - ci.yaml
  - deploy-private-nextflu.yaml
  - ingest-open.yaml
  - ingest.yaml
  - run-nextflu-private-builds.yaml
  - run-private-nextflu-builds.yaml
  - run-public-builds.yaml
  - upload.yaml
- dependabot.yml
- - README.md
- - reference_strains.txt
- - auspice_config.json
  - auspice_config_who.json
  - outliers.txt
  - reference_strains.txt
  - titer-strain-map.tsv
  - vaccine.json
- - reference_strains.txt
- - auspice_config.json
  - auspice_config_fitness.json
  - auspice_config_who.json
  - outliers.txt
  - reference_strains.txt
  - titer-strain-map.tsv
  - vaccine.json
- - auspice_config.json
  - auspice_config_who.json
  - outliers.txt
  - reference_strains.txt
  - titer-strain-map.tsv
  - vaccine.json
- - auspice_config.json
  - outliers.txt
  - reference_strains.txt
  - titer-strain-map.tsv
  - vaccine.json
- clades_for_titer_plots_h1n1pdm.txt
- clades_for_titer_plots_h3n2.txt
- clades_for_titer_plots_vic.txt
- color_schemes.tsv
- colors.tsv
- colors_for_titer_plots_h1n1pdm.tsv
- colors_for_titer_plots_h3n2.tsv
- colors_for_titer_plots_vic.tsv
- config.json
- description.md
- distance_maps.tsv
- frequency_weights_by_region.json
- geo_regions.tsv
- geo_synonyms.tsv
- ha_masks.tsv
- hi_titer_count_colors.tsv
- lat_longs.tsv
- mask_config.tsv
- na_masks.tsv
- nextstrain_clades_h1n1pdm_ha.tsv
- nextstrain_clades_h3n2_ha.tsv
- nextstrain_clades_vic_ha.tsv
- nextstrain_clades_yam_ha.tsv
- references_to_exclude_in_titer_plots_h1n1pdm.txt
- references_to_exclude_in_titer_plots_h3n2.txt
- references_to_exclude_in_titer_plots_vic.txt
- references_to_include_in_titer_plots_h1n1pdm.txt
- references_to_include_in_titer_plots_h3n2.txt
- references_to_include_in_titer_plots_vic.txt
- subclades_for_titer_plots_h1n1pdm.txt
- subclades_for_titer_plots_h3n2.txt
- subclades_for_titer_plots_vic.txt
- cdc_h3n2_cell_fra_titers.tsv
- cdc_h3n2_cell_hi_titers.tsv
- h3n2_ha.fasta
- h3n2_metadata.tsv
- h3n2_na.fasta
- haplotypes.tsv
- - calculate_clade_frequency_forecasts.py
  - calculate_delta_frequency.py
  - calculate_target_distances.py
  - calculate_weighted_distances.py
  - convert_translations_to_json.py
  - merge_weighted_distances_to_future.py
  - node_data_to_table.py
  - pairwise_titer_tree_distances.py
  - prepare_zoltar_predictions.py
- - cross_immunity.py
  - fit_model.py
  - forecast_model.py
  - weighted_distances.py
- 01-search-gisaid-for-h3n2.png
- 02-gisaid-search-results.png
- 03-download-metadata.png
- 04-download-sequences.png
- - config.yaml
  - exclude.txt
  - final_annotations.tsv
  - geolocation_rules.tsv
  - gisaid_location_rules.tsv
  - lineages.tsv
  - locations.tsv
  - strain_name_fixes.tsv
- - match-strain-names-via-epi-isl.py
  - strain-name-updates.md
  - strain-name-updates.snakefile
  - strain-name-updates.yaml
  - update-strains.py
- - curate.smk
  - nextclade.smk
  - prepare_ndjson.smk
- - annotate-with-gihsn
  - annotate-with-passage-category
  - curate-age
  - curate-gender
  - curate-host
  - dedup-by-gisaid-id
  - diff-avian-flu.py
  - diff-ndjson
  - filter-ndjson
  - filter-ndjson-by-value
  - link-gisaid-metadata-and-fasta
  - lowercase-fields
  - parse-gisaid-location
  - prioritize-id-per-strain
  - split-ndjson-by-segment
  - standardize-lineage
  - standardize-strain-names
- curation-docs.md
- README.md
- Snakefile
- - annotations.tsv
  - config.yaml
- - curate.smk
  - fetch.smk
  - nextclade.smk
- - link-metadata-and-sequences
  - parse-genspectrum-division
  - standardize-strain-name
- README.md
- Snakefile
- cell_fra_cTiter_x-ne_star.json
- cTiter_x-ne_star.json
- fra_cTiter_x-ne_star.json
- human_cell_fra_cTiter_x-ne_star.json
- human_cell_hi_cTiter_x-ne_star.json
- ne_star-lbi.json
- welsh_escape.json
- nextstrain-cdc.md.jinja
- - auspice_config.json
  - config_dict.yaml
  - human-nai-marker-table_for-publication_final_20240918.pdf
  - pa-marker-who-table_07-08-2024_updated_final-version.pdf
  - pathogen.json
- - adjust_pathogenjson.py
  - extract_founder_sequences.py
  - merge_jsons.py
- Snakefile
- 2022-07-26-plot-counts-per-lineage.ipynb
- 2023-12-15-identify-epitope-sites-and-scores-from-Welsh-et-al-data.ipynb
- 2025-07-08-create-distance-maps-for-Yu-et-al-phenotypes.py
- 2025-09-16-plot-ga-by-antigenic-advance.py
- 2026-02-19-plot-ga-by-antigenic-advance.py
- pairwise-antigenic-distance.py
- pick_library_strains.py
- README.md
- - builds.yaml
  - config.yaml
  - h1n1pdm_include.txt
  - h3n2_include.txt
  - vic_include.txt
  - yam_include.txt
- - builds.yaml
- - builds.yaml
  - config.yaml
- - builds.yaml
  - config.yaml
- - export.smk
  - h1n1pdm_all_human_prevax_2025.tsv
  - h1n1pdm_titer_strains.txt
  - h3n2_all_human_prevax_2025.tsv
  - h3n2_titer_strains.txt
- - builds.yaml
  - config.yaml
- - design_library.smk
  - h1n1pdm_recurrent_substitutions.json
  - h3n2_recurrent_substitutions.json
- - antigenic_distances.smk
  - deploy.smk
  - README.md
  - report.smk
- - rename.smk
  - zoltar.smk
- - builds.yaml
  - config.yaml
- - deploy.smk
  - rename.smk
- - export.smk
- - cluster.json
  - config.yaml
  - submit.sh
- - upload.smk
- full-trees.yaml
- neut-library.yaml
- nextflu-private-forecasts.yaml
- nextflu-private.yaml
- nextstrain-public-yamagata.yaml
- nextstrain-public.yaml
- private.nextflu.org.yaml
- quickstart-all-subtypes.yaml
- upload.yaml
- __init__.py
- add_derived_haplotypes.py
- annotate_derived_haplotypes.py
- annotate_titers_per_node.py
- assign_haplotypes.py
- calculate_antigenic_advance.py
- calculate_epiweek.py
- calculate_lcr_sum.py
- calculate_titer_distance_from_candidates.py
- combine-missing-titer-strains-tsvs.py
- construct-recency-from-submission-date.py
- count_recent_tips_by_clade.py
- create_narrative.py
- entropy.py
- estimate_frequencies_from_metadata.py
- export_titers_for_auspice_v1.py
- flag_outliers.py
- flu_regions.py
- forecast_frequencies_to_table.py
- frequencies_to_table.py
- generate_collection_config_json.py
- generate_locations_file.py
- generate_scale_for_coloring.py
- get_antigenic_distances_between_strains.py
- global_frequencies.py
- glyc.py
- graph_frequencies.py
- import_tip_clades.py
- intersect_items.py
- join_metadata.py
- join_tables.py
- make-branch-length-json.py
- mutation_statistics.py
- parse-json.py
- plot_antigenic_distances_between_strains.py
- plot_counts_per_lineage.py
- plot_forecast_tables.py
- plot_titer_matrices.py
- prepare_library_haplotypes.py
- prune_reference.py
- remap-titer-strain-names.py
- sanitize_trees.py
- scores.py
- sequence_export.py
- sha256sum
- summarize_haplotype_titer_coverage.py
- summarize_haplotypes.py
- summarize_haplotypes_for_library_design.py
- table_to_node_data.py
- titer-matching-viz.py
- vaccination_coverage.py
- - .gitrepo
  - .pre-commit-config.yaml
  - .shellcheckrc
  - README.md
- 2018_Europe_flu_vaccination_coverage.tsv
- 2018_OECD_flu_vaccination_coverage.csv
- 2018_South_America_flu_vaccination_coverage.tsv
- country_codes.tsv
- - nextstrain.yaml
  - notebook.yaml
- - array_builds.smk
  - common.smk
  - core.smk
  - download_from_fauna.smk
  - download_from_s3.smk
  - export.smk
  - fitness.smk
  - merge_inputs.smk
  - select_strains.smk
  - titer_models.smk
  - treeknit.smk
- project.json
.gitattributes
.gitignore
.pylintrc
CHANGES.md
nextstrain-pathogen.yaml
README.md
Snakefile

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