├── .browserslistrc ├── .cloudsql_env ├── .dockerignore ├── .editorconfig ├── .eslintignore ├── .gcloudignore ├── .gitattributes ├── .github └── workflows │ └── main.yml ├── .gitignore ├── .npmrc ├── .watchmanconfig ├── API.md ├── LICENSE ├── README.md ├── babel.config.js ├── config ├── config_flu_genbank.yaml ├── config_flu_genbank_dev.yaml ├── config_flu_gisaid.yaml ├── config_flu_gisaid_dev.yaml ├── config_rsv_custom.yaml ├── config_rsv_genbank.yaml ├── config_sars2_alpha.yaml ├── config_sars2_custom.yaml ├── config_sars2_genbank.yaml ├── config_sars2_genbank_dev.yaml ├── config_sars2_gisaid.yaml ├── config_sars2_gisaid_6month.yaml └── config_sars2_gisaid_private.yaml ├── docker-compose.cloudsql.prod.yml ├── docker-compose.cloudsql.yml ├── docker-compose.flu.genbank.yml ├── docker-compose.flu.gisaid.yml ├── docker-compose.rsv.yml ├── docker-compose.sars2.yml ├── docker-compose.yml ├── environment.yml ├── environment_osx-arm64.yml ├── example_data_genbank ├── flu.tar.gz ├── rsv.tar.gz └── sars2.tar.gz ├── jsconfig.json ├── package.json ├── package_example_data.sh ├── pymol ├── map_spike_snps.py ├── merge_pymol_interactions.py ├── pymol_color_spike_no_load.py ├── pymol_color_spike_snps.py ├── pymol_interacting_nab.py └── pymol_select_regions.py ├── services ├── frontend │ └── Dockerfile ├── postgres │ ├── Dockerfile │ ├── create_dbs.sh │ ├── postgres.conf │ └── test_queries │ │ └── coverage_tests.sql └── server │ ├── cg_server │ ├── __init__.py │ ├── app.py │ ├── auth.py │ ├── color.py │ ├── config.py │ ├── constants.py │ ├── db.py │ ├── db_seed │ │ ├── __init__.py │ │ ├── insert_sequences.py │ │ ├── load_mutations.py │ │ └── seed.py │ ├── dev_only.py │ ├── download │ │ ├── __init__.py │ │ ├── genomes.py │ │ └── metadata.py │ ├── gunicorn.conf.py │ ├── main.py │ ├── query │ │ ├── __init__.py │ │ ├── country_score.py │ │ ├── group_mutation_frequencies.py │ │ ├── initial.py │ │ ├── metadata.py │ │ ├── report.py │ │ ├── selection.py │ │ └── variant_table.py │ ├── routes │ │ ├── __init__.py │ │ ├── download.py │ │ ├── query.py │ │ ├── report.py │ │ ├── seed.py │ │ └── views.py │ └── test_connpool.py │ ├── cloudsql.Dockerfile │ ├── dev.Dockerfile │ ├── prod.Dockerfile │ ├── requirements.txt │ └── serve.sh ├── src ├── assets │ ├── analysis_screens │ │ ├── d614g_europe_na.png │ │ ├── d614g_us_states.png │ │ ├── d614g_west_coast.png │ │ ├── global_lineages.png │ │ ├── iceland.png │ │ ├── n_203_204_coocurrence.png │ │ ├── us_cdc_primer.png │ │ └── xinfadi.png │ ├── example_screens │ │ ├── example1_1.png │ │ ├── example1_2.png │ │ ├── example1_3.png │ │ ├── example1_4.png │ │ ├── example2_1.png │ │ ├── example2_2.png │ │ ├── example2_3.png │ │ ├── example2_4.png │ │ ├── example3_1.png │ │ ├── example3_2.png │ │ └── example3_3.png │ └── images │ │ ├── BroadLogo_RGB_forDigital.png │ │ ├── CVRBioInfo_logo.png │ │ ├── Fig2_workflow_V4.svg │ │ ├── Fig2_workflow_V5.svg │ │ ├── HKUST-original_0.svg │ │ ├── React-icon.svg │ │ ├── VE_logo_new.png │ │ ├── cg_logo_v13.pdf │ │ ├── cg_logo_v13.png │ │ ├── cg_logo_v13.svg │ │ ├── cg_logo_v13@2x.png │ │ ├── cg_logo_v13@4x.png │ │ ├── cg_short_v13.pdf │ │ ├── cg_short_v13.png │ │ ├── cg_short_v13.svg │ │ ├── cg_short_v13@2x.png │ │ ├── cg_short_v13@4x.png │ │ ├── cg_short_v13@4x_square.png │ │ ├── csiro_logo.png │ │ ├── favicon │ │ ├── android-chrome-192x192.png │ │ ├── android-chrome-512x512.png │ │ ├── apple-touch-icon.png │ │ ├── favicon-16x16.png │ │ ├── favicon-32x32.png │ │ ├── favicon.ico │ │ └── site.webmanifest │ │ ├── flu_pathmut_logo_v1.pdf │ │ ├── flu_pathmut_logo_v1.png │ │ ├── flu_pathmut_logo_v1.svg │ │ ├── flu_pathmut_logo_v1@2x.png │ │ ├── flu_pathmut_logo_v1@4x.png │ │ ├── gisaid_logo.png │ │ ├── idl-logo.png │ │ ├── jhu_logo.jpg │ │ ├── kaust_logo.png │ │ ├── lanl_logo.svg │ │ ├── logo-cog-uk.png │ │ ├── mobx.png │ │ ├── mrc_logo.png │ │ ├── ncbi_logo.svg │ │ ├── nextstrain_logo.png │ │ ├── niaid_logo.png │ │ ├── pangolin_logo.png │ │ ├── polimi_logo.png │ │ ├── rdg-logo.png │ │ ├── react_slingshot.png │ │ ├── rsv_pathmut_logo_v1.pdf │ │ ├── rsv_pathmut_logo_v1.png │ │ ├── rsv_pathmut_logo_v1.svg │ │ ├── rsv_pathmut_logo_v1@2x.png │ │ ├── rsv_pathmut_logo_v1@4x.png │ │ ├── rsvg_logo_temp.pdf │ │ ├── rsvg_logo_temp.png │ │ ├── ubc_logo.png │ │ ├── ucscHelixLogo.png │ │ ├── uglasgow_logo.png │ │ ├── university-college-london-ucl-vector-logo.svg │ │ ├── ve_logo.png │ │ ├── vipr_logo.png │ │ ├── vipr_logo@4x.png │ │ ├── virusurf_logo.png │ │ └── wustl_virusgateway.svg ├── components │ ├── App.js │ ├── Buttons │ │ ├── Button.js │ │ ├── Button.styles.js │ │ ├── DeselectButton.js │ │ ├── DropdownButton.js │ │ ├── DropdownButton.styles.js │ │ ├── GenotypeToggleButton.js │ │ └── QuestionButton.js │ ├── Cells │ │ ├── AckAuthorCell.js │ │ ├── AckCell.js │ │ ├── GroupCell.js │ │ ├── HeatmapCell.js │ │ ├── LetterCell.js │ │ └── PosHeaderCell.js │ ├── Common │ │ ├── Accordion.styles.js │ │ ├── AccordionWrapper.js │ │ ├── AcknowledgementFooter.js │ │ ├── AcknowledgementFooter.styles.js │ │ ├── EmptyPlot.js │ │ ├── ExternalLink.js │ │ ├── KBD.js │ │ ├── LineageName.js │ │ ├── LineageName.styles.js │ │ ├── LoadingSpinner.js │ │ ├── LoadingSpinner.styles.js │ │ ├── NothingSelected.js │ │ ├── NothingSelected.styles.js │ │ ├── SelectBoxText.js │ │ ├── SkeletonElement.js │ │ ├── SkeletonElement.styles.js │ │ ├── StyledDropdownTreeSelect.js │ │ ├── TabIndicator.js │ │ ├── TabIndicator.styles.js │ │ ├── WarningBox.js │ │ └── WarningBox.styles.js │ ├── Example │ │ ├── ExampleList.js │ │ ├── ExampleList.styles.js │ │ ├── WalkthroughList.js │ │ └── WalkthroughList.styles.js │ ├── GroupReport │ │ ├── GroupReportHeader.js │ │ ├── GroupReportHeader.styles.js │ │ ├── GroupSearch.js │ │ ├── GroupSearch.styles.js │ │ ├── GroupStructuralViewer.js │ │ ├── GroupStructuralViewer.styles.js │ │ ├── MutationList.js │ │ ├── MutationList.styles.js │ │ ├── MutationList.utils.js │ │ ├── OrgLegend.js │ │ ├── OrgLegend.styles.js │ │ ├── SelectedReportGroups.js │ │ ├── SelectedReportGroups.styles.js │ │ ├── VOCList.js │ │ └── VOCList.styles.js │ ├── KeyListener.js │ ├── Legend │ │ ├── Legend.styles.js │ │ ├── LegendContainer.js │ │ ├── TableLegend.js │ │ ├── TableLegend.styles.js │ │ ├── TableLegendItem.js │ │ ├── TableLegendItem.styles.js │ │ └── legendUtils.js │ ├── LiteMol │ │ ├── LiteMolPlugin.js │ │ ├── StructureEntities.js │ │ ├── StructureEntities.styles.js │ │ └── litemolutils.js │ ├── LoadingScreen.js │ ├── LoadingScreen.styles.js │ ├── Modals │ │ ├── AsyncErrorModal.js │ │ ├── DownloadConsensusMutationsModal.js │ │ ├── DownloadGenomesModal.js │ │ ├── DownloadMetadataModal.js │ │ ├── DownloadPymolScriptModal.js │ │ ├── DownloadVariantTableModal.js │ │ ├── Modal.styles.js │ │ ├── SelectSequencesModal.js │ │ ├── SelectSequencesModal.styles.js │ │ └── SplashScreenModal.js │ ├── Pages │ │ ├── AboutTabFlu.js │ │ ├── AboutTabRSV.js │ │ ├── AboutTabSARS.js │ │ ├── CompareGroupsTab.js │ │ ├── CompareLocationsTab.js │ │ ├── GroupReportTab.js │ │ ├── GroupReportTab.styles.js │ │ ├── HomeTab.js │ │ ├── HomeTab.styles.js │ │ ├── MainPage.js │ │ ├── MainPage.styles.js │ │ ├── MethodologyTab.js │ │ ├── NotFoundPage.js │ │ ├── RelatedProjectsTab.js │ │ ├── SequencingEffortsTab.js │ │ ├── SequencingEffortsTab.styles.js │ │ └── TextTab.styles.js │ ├── Selection │ │ ├── CoordinateSelect.js │ │ ├── CoordinateSelect.styles.js │ │ ├── DateSelect.js │ │ ├── DateSelect.styles.js │ │ ├── GroupBySelect.js │ │ ├── GroupBySelect.styles.js │ │ ├── GroupSelect.js │ │ ├── GroupSelect.styles.js │ │ ├── LocationSelect.js │ │ ├── LocationSelect.styles.js │ │ ├── MetaFieldSelect.js │ │ ├── MetaFieldSelect.styles.js │ │ ├── QualitySelect.js │ │ ├── QualitySelect.styles.js │ │ ├── SelectionTopBar.js │ │ └── SelectionTopBar.styles.js │ ├── Sidebar │ │ ├── DefaultSidebar.js │ │ ├── DefaultSidebar.styles.js │ │ ├── DownloadDataButton.js │ │ ├── DownloadDataButton.styles.js │ │ ├── FilterSidebar.js │ │ ├── FilterSidebar.styles.js │ │ ├── Footer.js │ │ ├── Footer.styles.js │ │ ├── Header.js │ │ ├── Header.styles.js │ │ ├── StatusBox.js │ │ ├── StatusBox.styles.js │ │ ├── TabBar.js │ │ └── TabBar.styles.js │ ├── Viz │ │ ├── CooccurrencePlot.js │ │ ├── EntropyPlot.js │ │ ├── GlobalSeqPlot.js │ │ ├── GradientLegend.js │ │ ├── GradientLegend.styles.js │ │ ├── GroupStackPlot.js │ │ ├── GroupStackPlot.styles.js │ │ ├── GroupTreePlot.js │ │ ├── GroupTreePlot.styles.js │ │ ├── LocationDatePlot.js │ │ ├── LocationGroupPlot.js │ │ ├── LowFreqFilter.js │ │ ├── LowFreqFilter.styles.js │ │ ├── MarkLegend.js │ │ ├── MarkLegend.styles.js │ │ ├── MutationStructureViewer.js │ │ ├── MutationStructureViewer.styles.js │ │ ├── NumSeqPerLocationBar.js │ │ ├── NumSeqPerLocationLine.js │ │ ├── Plot.styles.js │ │ ├── SequencingMapPlot.js │ │ ├── SurveillancePlot.js │ │ └── SurveillancePlot.styles.js │ └── WaitForAsyncWrapper.js ├── config │ └── index.js ├── constants │ ├── colors.js │ ├── defs.json │ ├── functions.js │ ├── initialValues.js │ └── metadata.js ├── examples │ ├── examples.flu.js │ ├── examples.rsv.js │ ├── examples.sars2.js │ └── index.js ├── favicon.ico ├── fonts │ ├── fontello.eot │ ├── fontello.svg │ ├── fontello.ttf │ ├── fontello.woff │ └── fontello.woff2 ├── index.ejs ├── index.js ├── react_vega │ ├── LICENSE │ ├── VegaEmbed.js │ └── utils │ │ ├── computeSpecChanges.js │ │ ├── getDatasetNamesFromSpec.js │ │ ├── getUniqueFieldNames.js │ │ ├── isFunction.js │ │ └── shallowEqual.js ├── routes.js ├── stores │ ├── UIStore.js │ ├── asyncDataStore.js │ ├── configStore.js │ ├── connect.js │ ├── dataStore.js │ ├── globalSequencingData.js │ ├── groupDataStore.js │ ├── locationDataStore.js │ ├── metadataStore.js │ ├── mutationData.js │ ├── plotSettingsStore.js │ ├── rootStore.js │ ├── surveillanceDataStore.js │ └── urlMonitor.js ├── styles │ └── litemol.min.css ├── utils │ ├── color.js │ ├── coordinates.js │ ├── data.js │ ├── date.js │ ├── device.js │ ├── download.js │ ├── example.worker.js │ ├── exampleWorkerWrapper.js │ ├── func.js │ ├── gene_protein.js │ ├── location.js │ ├── math.js │ ├── mutationData.worker.js │ ├── mutationDataWorkerWrapper.js │ ├── mutationUtils.js │ ├── primer.js │ ├── pymol.js │ ├── reference.js │ ├── string.js │ ├── transform.js │ ├── updateQueryParam.js │ └── version.js ├── vega_specs │ ├── area_stack.vl.json │ ├── area_stack_simulated_standalone.json │ ├── area_stack_standalone.vl.json │ ├── barplot_v2.vl.json │ ├── barplot_v3.vl.json │ ├── cooccurrence_plot.vg.json │ ├── cooccurrence_plot_standalone.vg.json │ ├── entropy.vg.json │ ├── entropy_standalone.vg.json │ ├── global_seq_v2.vg.json │ ├── group_stack.vg.json │ ├── group_stack_standalone.vg.json │ ├── group_tree_legend_v2.vg.json │ ├── group_tree_v1.vg.json │ ├── group_tree_v2.vg.json │ ├── location_date.vg.json │ ├── location_date_standalone.vg.json │ ├── location_group.vg.json │ ├── location_group_standalone.vg.json │ ├── map_combined.vg.json │ ├── map_combined_standalone.vg.json │ ├── map_sequences_per_case_standalone.vg.json │ ├── map_turnaround_time_standalone.vg.json │ ├── num_seq_per_location_bar.standalone.vg.json │ ├── num_seq_per_location_bar.vg.json │ ├── num_seq_per_location_line.standalone.vg.json │ ├── num_seq_per_location_line.vg.json │ ├── surveillance.vg.json │ └── surveillance_standalone_rsv.vg.json └── webpack-public-path.js ├── static_data ├── flu │ ├── alignments │ │ ├── .sglock │ │ │ ├── H3N2_4_NC_007366.dna=hotdog.local=77771 │ │ │ ├── H3N2_6_NC_007368.dna=hotdog.local=77771 │ │ │ └── H3N2_7_NC_007367.dna=hotdog.local=77771 │ │ ├── B-vic_1_JN600474.dna │ │ ├── B-vic_2_JN600475.dna │ │ ├── B-vic_3_JN600476.dna │ │ ├── B-vic_4_FLBHAAA.dna │ │ ├── B-vic_5_JN600477.dna │ │ ├── B-vic_6_AB036870.dna │ │ ├── B-vic_7_JN600478.dna │ │ ├── B-vic_8_JN600479.dna │ │ ├── B-yam_1_AF101989.dna │ │ ├── B-yam_2_AF102006.dna │ │ ├── B-yam_3_AF102023.dna │ │ ├── B-yam_4_MK715607.dna │ │ ├── B-yam_5_FLBIBNA.dna │ │ ├── B-yam_6_AY139081.dna │ │ ├── B-yam_7_AF100378.dna │ │ ├── B-yam_8_AF100396.dna │ │ ├── H10N8_1.dna │ │ ├── H10N8_2.dna │ │ ├── H10N8_3.dna │ │ ├── H10N8_4.dna │ │ ├── H10N8_5.dna │ │ ├── H10N8_6.dna │ │ ├── H10N8_7.dna │ │ ├── H10N8_8.dna │ │ ├── H1N1_1_MZ310486.dna │ │ ├── H1N1_2_MZ310487.dna │ │ ├── H1N1_3_MZ310488.dna │ │ ├── H1N1_4_MZ310489.dna │ │ ├── H1N1_5_MZ310490.dna │ │ ├── H1N1_6_MZ310491.dna │ │ ├── H1N1_7_NC_002016.dna │ │ ├── H1N1_8_MZ310493.dna │ │ ├── H3N2_1_NC_007373.1.dna │ │ ├── H3N2_2_NC_007372.1.dna │ │ ├── H3N2_3_NC_007371.1.dna │ │ ├── H3N2_4_NC_007366.1.dna │ │ ├── H3N2_5_NC_007369.1.dna │ │ ├── H3N2_6_NC_007368.1.dna │ │ ├── H3N2_7_NC_007367.1.dna │ │ ├── H3N2_8_NC_007370.1.dna │ │ ├── H5N1_1_NC_007357.dna │ │ ├── H5N1_2_NC_007358.dna │ │ ├── H5N1_3_NC_007359.dna │ │ ├── H5N1_4_NC_007362.dna │ │ ├── H5N1_5_NC_007360.dna │ │ ├── H5N1_6_NC_007361.dna │ │ ├── H5N1_7_NC_007363.dna │ │ ├── H5N1_8_NC_007364.dna │ │ ├── H7N2_1_NC_026422.dna │ │ ├── H7N2_2_NC_026423.dna │ │ ├── H7N2_3_NC_026424.dna │ │ ├── H7N2_4_NC_026425.dna │ │ ├── H7N2_5_NC_026426.dna │ │ ├── H7N2_6_NC_026429.dna │ │ ├── H7N2_7_NC_026427.dna │ │ ├── H7N2_8_NC_026428.dna │ │ ├── H9N2_1_NC_004910.dna │ │ ├── H9N2_2_NC_004911.dna │ │ ├── H9N2_3_NC_004912.dna │ │ ├── H9N2_4_NC_004908.dna │ │ ├── H9N2_5_NC_004905.dna │ │ ├── H9N2_6_NC_004909.dna │ │ ├── H9N2_7_NC_004907.dna │ │ ├── H9N2_8_NC_004906.dna │ │ └── HA_all.praln │ ├── country_to_emoji.xls │ ├── default_structures.json │ ├── genes.csv │ ├── genes_processed.json │ ├── location_corrections.csv │ ├── mut_references │ │ ├── B-vic │ │ │ ├── B-Austria-1359417-2021 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── B-Brisbane-60-2008 │ │ │ │ ├── 4.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── B-Colorado-06-2017 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ └── DESCRIPTION │ │ │ └── B-Washington-02-2019 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ ├── B-yam │ │ │ ├── B-Massachusetts-02-2012 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── B-Phuket-3073-2013 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ └── B-Wisconsin-01-2010 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ ├── H10NX │ │ │ ├── A-Jiangsu-428-2021 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ │ └── A-Jiangxi-Donghu-346-2013 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ ├── H1N1 │ │ │ ├── A-Brisbane-02-2018 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-California-07-2009 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Guangdong-Maonan-SWL1536-2019 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Michigan-45-2015 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Victoria-2570-2019 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ └── A-Wisconsin-67-2022 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ ├── H3N2 │ │ │ ├── A-Cambodia-e0826360-2020 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Darwin-6-2021 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ │ ├── A-Darwin-9-2021 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Hong-Kong-4801-2014 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Kansas-14-2017 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Perth-16-2009 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Singapore-INFIMH-16-0019-2016 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Switzerland-9715293-2013 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ ├── A-Texas-50-2012 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ └── DESCRIPTION │ │ │ └── A-Victoria-361-2011 │ │ │ │ ├── 4.fa │ │ │ │ ├── 6.fa │ │ │ │ └── DESCRIPTION │ │ ├── H5NX │ │ │ ├── A-Goose-Guangdong-1-96 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ │ └── A-Viet-Nam-1203-2004 │ │ │ │ ├── 4.fa │ │ │ │ └── DESCRIPTION │ │ ├── H7NX │ │ │ ├── A-Anhui-1-2013 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ │ └── A-Shanghai-02-2013 │ │ │ │ ├── 1.fa │ │ │ │ ├── 2.fa │ │ │ │ ├── 3.fa │ │ │ │ ├── 4.fa │ │ │ │ ├── 5.fa │ │ │ │ ├── 6.fa │ │ │ │ ├── 7.fa │ │ │ │ ├── 8.fa │ │ │ │ ├── DESCRIPTION │ │ │ │ └── NOTES │ │ └── H9NX │ │ │ └── A-Hong-Kong-1073-99 │ │ │ ├── 1.fa │ │ │ ├── 2.fa │ │ │ ├── 3.fa │ │ │ ├── 4.fa │ │ │ ├── 5.fa │ │ │ ├── 6.fa │ │ │ ├── 7.fa │ │ │ ├── 8.fa │ │ │ ├── DESCRIPTION │ │ │ └── NOTES │ ├── primers.csv │ ├── primers.json │ ├── proteins.csv │ ├── proteins_processed.json │ ├── reference.json │ ├── serotype_references │ │ ├── 1.fa │ │ ├── 2.fa │ │ ├── 3.fa │ │ ├── 4.fa │ │ ├── 5.fa │ │ ├── 6.fa │ │ ├── 7.fa │ │ └── 8.fa │ └── world-110m-mod.json ├── rsv │ ├── country_to_emoji.xls │ ├── default_structures.json │ ├── genes.csv │ ├── genes_processed.json │ ├── genotype_references.fasta │ ├── genotype_references.json │ ├── genotypesBySubtype.json │ ├── mut_references │ │ ├── A │ │ │ ├── KX858757.1 │ │ │ │ ├── 1.fa │ │ │ │ └── DESCRIPTION │ │ │ └── NC_038235.1 │ │ │ │ ├── 1.fa │ │ │ │ └── DESCRIPTION │ │ └── B │ │ │ ├── KX858756.1 │ │ │ ├── 1.fa │ │ │ └── DESCRIPTION │ │ │ └── NC_001781.1 │ │ │ ├── 1.fa │ │ │ └── DESCRIPTION │ ├── old │ │ ├── A.fa │ │ ├── A │ │ │ ├── KX858757.1.fa │ │ │ └── NC_038235.1.fa │ │ ├── B.fa │ │ └── B │ │ │ ├── KX858756.1.fa │ │ │ └── NC_001781.1.fa │ ├── primers.csv │ ├── primers.json │ ├── proteins.csv │ ├── proteins_processed.json │ ├── reference.fa │ ├── reference.json │ ├── vocs.json │ └── world-110m-mod.json └── sars2 │ ├── CDC.json │ ├── ECDC.json │ ├── PHE.json │ ├── WHO.json │ ├── artic_primers.csv │ ├── country_to_emoji.xls │ ├── default_structures.json │ ├── genbank_field.txt │ ├── genes.csv │ ├── genes_processed.json │ ├── location_corrections.csv │ ├── mut_references │ └── SARS-CoV-2 │ │ └── WIV04 │ │ ├── 1.fa │ │ └── DESCRIPTION │ ├── nextstrain_exclude_20200520.txt │ ├── primers.csv │ ├── primers.json │ ├── proteins.csv │ ├── proteins_processed.json │ ├── reference.json │ ├── vocs.json │ └── world-110m-mod.json ├── tools ├── .yarnclean ├── analyzeBundle.js ├── build.js ├── chalkConfig.js ├── distServer.js ├── fileMock.js ├── loadConfigFile.js ├── nodeVersionCheck.js ├── srcServer.js └── startMessage.js ├── tsconfig.json ├── webpack.config.dev.js ├── webpack.config.prod.js ├── workflow_flu_genbank_ingest ├── README.md ├── Snakefile └── scripts │ ├── LICENSE_NEXTSTRAIN │ ├── chunk_sequences.py │ ├── clean_metadata.py │ ├── copy_changed_files.py │ ├── download_metadata.py │ ├── download_sequences.py │ ├── join_serotype_assignments.py │ ├── location_cleaning.ipynb │ ├── make_ref_json.py │ ├── make_references.py │ ├── sequence_quality.py │ └── write_ha_fasta.py ├── workflow_flu_gisaid_ingest ├── README.md ├── Snakefile └── scripts │ ├── chunk_sequences.py │ ├── clean_metadata.py │ └── copy_changed_files.py ├── workflow_main ├── Snakefile ├── analyses │ ├── Snakefile │ └── scripts │ │ ├── __init__.py │ │ ├── az_report.py │ │ ├── consensus_mutations.py │ │ ├── global_seq_data.py │ │ ├── global_sequencing_efforts.py │ │ ├── mutation_frequency_report.py │ │ ├── standalone_map_spec.py │ │ └── surveillance.py ├── phylotree │ ├── LICENSE_COVIZU │ ├── Snakefile │ └── scripts │ │ ├── __init__.py │ │ ├── build_graph_table.py │ │ └── representative_seqs.py └── scripts │ ├── __init__.py │ ├── abbreviate_authors.py │ ├── artic_primers.py │ ├── assemble_data_package.py │ ├── bam_subseq.py │ ├── build_full_dataframe.py │ ├── build_location_tree.py │ ├── collapse_to_isolate.py │ ├── combine_all_data.py │ ├── combine_coverage.py │ ├── combine_coverage_pivot.py │ ├── coverage_aa.py │ ├── coverage_dna.py │ ├── extract_aa_mutations.py │ ├── extract_dna_mutations.py │ ├── fasta.py │ ├── gene_protein_defs.py │ ├── get_cdc_vocs.py │ ├── get_ecdc_vocs.py │ ├── get_phe_vocs.py │ ├── get_who_vocs.py │ ├── global_group_counts.py │ ├── preprocess_rsv_sequences.py │ ├── preprocess_sars2_sequences.py │ ├── process_mutations.py │ ├── push_to_database.py │ ├── read_extractor_lite.py │ ├── send_email.py │ ├── sequence_manifest.py │ ├── touch_bam.py │ ├── update_vocs.py │ ├── util.py │ └── write_reference_files.py ├── workflow_rsv_custom_ingest ├── README.md ├── Snakefile ├── scripts │ └── clean_metadata.py └── test_data │ └── data_custom │ ├── fasta_raw │ └── 1985-02-20.fa.gz │ └── metadata_raw.csv ├── workflow_rsv_genbank_ingest ├── README.md ├── Snakefile └── scripts │ ├── LICENSE_NEXTSTRAIN │ ├── chunk_sequences.py │ ├── clean_metadata.py │ ├── copy_changed_files.py │ ├── download_metadata.py │ ├── download_sequences.py │ ├── join_subtype_assignments.py │ ├── sequence_quality.py │ ├── split_sequences_by_subtype.py │ └── write_all_fasta.py ├── workflow_sars2_custom_ingest ├── README.md ├── Snakefile ├── envs │ └── pangolin.yaml ├── scripts │ ├── clean_metadata.py │ └── combine_lineages.py └── test-data │ └── data_custom │ ├── fasta_raw │ └── test-sequences.fa.gz │ └── metadata_raw.csv ├── workflow_sars2_genbank_ingest ├── README.md ├── Snakefile ├── envs │ └── 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