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Merge pull request #126 from nextstrain/james/D1.1-genome
H5N1 D1.1 genome build
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| # | ||
| # TKTK | ||
| # | ||
| custom_rules: | ||
| - "rules/cattle-flu.smk" | ||
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| #### Parameters which define which builds to produce via this config ### | ||
| builds: | ||
| h5n1-d1.1: '' | ||
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| segments: | ||
| - genome | ||
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| # Input source(s) - See README.md for how to use local files instead and/or add additional inputs | ||
| inputs: | ||
| - name: ncbi | ||
| metadata: s3://nextstrain-data/files/workflows/avian-flu/h5n1/metadata.tsv.zst | ||
| sequences: s3://nextstrain-data/files/workflows/avian-flu/h5n1/{segment}/sequences.fasta.zst | ||
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| #### Parameters which control large overarching aspects of the build | ||
| # Set a high target_sequences_per_tree to capture all circulating strains, as they will be pruned down | ||
| # as part of the workflow | ||
| target_sequences_per_tree: 10_000 | ||
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| #### Config files #### | ||
| reference: config/h5n1/reference_h5n1_{segment}.gb # use H5N1 references | ||
| genome_reference: config/h5n1-cattle-outbreak/h5_cattle_genome_root.gb # use cattle-flu genome reference TODO XXX | ||
| auspice_config: config/{subtype}/auspice_config_{subtype}.json | ||
| colors: config/h5n1/colors_h5n1.tsv # use H5N1 colors | ||
| lat_longs: config/h5n1/lat_longs_h5n1.tsv # use H5N1 lat-longs | ||
| include_strains: config/{subtype}/include_strains_{subtype}.txt | ||
| # use cattle-outbreak specific dropped strains for segment + genome trees | ||
| dropped_strains: config/{subtype}/dropped_strains_{subtype}.txt | ||
| clades_file: clade-labeling/h5n1-clades.tsv # use H5N1 clades | ||
| description: config/{subtype}/description.md | ||
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| #### Rule-specific parameters #### | ||
| filter: | ||
| min_length: | ||
| FALLBACK: | ||
| pb2: 2100 | ||
| pb1: 2100 | ||
| pa: 2000 | ||
| ha: 1600 | ||
| np: 1400 | ||
| na: 1270 | ||
| mp: 900 | ||
| ns: 800 | ||
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| min_date: | ||
| FALLBACK: 2024 | ||
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| group_by: | ||
| FALLBACK: false # no grouping during filter | ||
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| exclude_where: | ||
| FALLBACK: host=laboratoryderived host=ferret host=unknown host=other host=host gisaid_clade=3C.2 | ||
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| mask: | ||
| min_support: 50 # This masks any position where <50% of sequences have a base | ||
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| refine: | ||
| coalescent: const | ||
| date_inference: marginal | ||
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| genome_clock_filter_iqd: | ||
| FALLBACK: 6 | ||
| clock_filter_iqd: | ||
| FALLBACK: false | ||
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| root: | ||
| FALLBACK: false | ||
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| # For the genome only we use the closest outgroup as the root | ||
| # P.S. Make sure this strain is force included via augur filter --include | ||
| # (This isn't needed for the segment builds as we include a large enough time span to root via the clock) | ||
| genome_root: | ||
| FALLBACK: best | ||
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| segment_lengths: | ||
| FALLBACK: | ||
| {'pb2': 2341, 'pb1': 2341, 'pa': 2233, 'ha': 1760, 'np': 1565, 'na': 1458, 'mp': 1027, 'ns': 865} | ||
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| __clock_std_dev: &clock_std_dev 0.00211 # YAML anchor so we can reference this value below | ||
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| clock_rates: | ||
| FALLBACK: | ||
| # The rates for the 8 segments are taken from the GISAID H5N1/2y config | ||
| pb2: [0.00287, *clock_std_dev] | ||
| pb1: [0.00264, *clock_std_dev] | ||
| pa: [0.00248, *clock_std_dev] | ||
| ha: [0.00455, *clock_std_dev] | ||
| np: [0.00252, *clock_std_dev] | ||
| na: [0.00349, *clock_std_dev] | ||
| mp: [0.00191, *clock_std_dev] | ||
| ns: [0.00249, *clock_std_dev] | ||
| # the genome clock rate is calculated by a function in the snakemake pipeline | ||
| # using the segment rates weighted by their lengths | ||
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| ancestral: | ||
| inference: joint | ||
| root_seq: | ||
| FALLBACK: false | ||
| genome_root_seq: | ||
| FALLBACK: config/h5n1-cattle-outbreak/h5_cattle_genome_root.gb | ||
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| traits: | ||
| # genome build has different parameters... | ||
| genome_columns: | ||
| FALLBACK: division | ||
| genome_sampling_bias_correction: | ||
| FALLBACK: 5 | ||
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| # segment builds: | ||
| columns: | ||
| FALLBACK: region country # same as GISAID H5N1 builds | ||
| sampling_bias_correction: | ||
| FALLBACK: false | ||
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| # all builds | ||
| confidence: | ||
| FALLBACK: true | ||
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| export: | ||
| genome_title: | ||
| FALLBACK: false | ||
| title: | ||
| FALLBACK: false |
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| { | ||
| "title": "Full genome analysis of the ongoing influenza A/H5N1 D1.1 outbreak in North America", | ||
| "maintainers": [ | ||
| {"name": "Moncla lab", "url": "https://lmoncla.github.io/monclalab/"}, | ||
| {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"} | ||
| ], | ||
| "build_url": "https://github.com/nextstrain/avian-flu", | ||
| "data_provenance": [ | ||
| { | ||
| "name": "USDA", | ||
| "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1102327" | ||
| }, | ||
| { | ||
| "name": "Andersen Lab", | ||
| "url": "https://github.com/andersen-lab/avian-influenza/" | ||
| }, | ||
| { | ||
| "name": "GenBank", | ||
| "url": "https://www.ncbi.nlm.nih.gov/genbank/" | ||
| } | ||
| ], | ||
| "extensions": { | ||
| "nextclade": { | ||
| "pathogen": { | ||
| "schemaVersion":"3.0.0", | ||
| "defaultCds": "HA", | ||
| "cdsOrderPreference":[ | ||
| "PB2", | ||
| "PB1", | ||
| "PA", | ||
| "HA", | ||
| "NP", | ||
| "NA", | ||
| "M1", | ||
| "M2", | ||
| "NS1", | ||
| "NS2" | ||
| ], | ||
| "attributes": { | ||
| "name": "H5N1 D1.1 Genome analysis", | ||
| "reference name": "concatenated ancestral sequences", | ||
| "reference accession": "none" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "colorings": [ | ||
| { | ||
| "key": "gt", | ||
| "title": "Genotype", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "num_date", | ||
| "title": "Date", | ||
| "type": "continuous" | ||
| }, | ||
| { | ||
| "key": "region", | ||
| "title": "Region", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "country", | ||
| "title": "Country", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "division", | ||
| "title": "Admin Division", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "host", | ||
| "title": "Host", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "subtype", | ||
| "title": "Subtype", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "genoflu", | ||
| "title": "GenoFLU", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "h5_label_clade", | ||
| "title": "Provisional LABEL Clade", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "furin_cleavage_motif", | ||
| "title": "Furin Cleavage Motif", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "cleavage_site_sequence", | ||
| "title": "Cleavage Site Sequence", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "author", | ||
| "title": "Authors", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "originating_lab", | ||
| "title": "Originating Lab", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "submitting_lab", | ||
| "title": "Submitting Lab", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "data_source", | ||
| "title": "Data Source", | ||
| "type": "categorical" | ||
| } | ||
| ], | ||
| "geo_resolutions": [ | ||
| "region", | ||
| "country", | ||
| "division" | ||
| ], | ||
| "display_defaults": { | ||
| "map_triplicate": false, | ||
| "color_by": "host", | ||
| "geo_resolution": "division", | ||
| "distance_measure": "div", | ||
| "panels": ["tree", "entropy"] | ||
| }, | ||
| "filters": [ | ||
| "host", | ||
| "region", | ||
| "country", | ||
| "division", | ||
| "subtype", | ||
| "author", | ||
| "originating_lab", | ||
| "submitting_lab", | ||
| "data_source" | ||
| ], | ||
| "metadata_columns": [ | ||
| "genbank_accession", | ||
| "sra_accessions" | ||
| ] | ||
| } |
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| We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain. | ||
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| Genomic data from the ongoing H5N1 outbreaks in the US was shared by the [National Veterinary Services Laboratories (NVSL)](https://www.aphis.usda.gov/labs/about-nvsl) of the [Animal and Plant Health Inspection Service (APHIS)](https://www.aphis.usda.gov/) of the U.S. Department of Agriculture (USDA) in an open fashion to NCBI GenBank (consensus genomes and complete metadata) and to the SRA (raw reads with redacted metadata) in [BioProject PRJNA1102327](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1102327). Other groups have contributed sequence data here, but the majority of viral genomes have been shared by the USDA. The Andersen Lab has assembled raw reads from this SRA BioProject and publicly shared consensus genomes to [GitHub](https://github.com/andersen-lab/avian-influenza). We thank the USDA for genomic data sharing and the Andersen Lab for sharing assembled consensus genomes. | ||
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| In this analysis, we've curated data from NCBI GenBank and merged this data with SRA data via the Andersen Lab GitHub repository. | ||
| We will make curated sequence & metadata files available shortly. Data source as GenBank vs SRA-via-Andersen-Lab is included in this metadata and is available as a [coloring to this page](?c=data_source). | ||
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| ### Limitations | ||
| Importantly, SRA-derived genomes only have the year of collection (e.g. 2024-XX-XX or 2025-XX-XX) and "USA" as collection location. In this analysis, we've inferred collection date and collection location for these samples along with confidence in date and location, however these must be treated with caution. We've added two colorings for geographic division: [one using inferred values](?c=division) and one only reporting [known values](?c=division_metadata). For these reasons we have toggled the map panel off by default. | ||
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| In addition to this cattle outbreak specific view, we have broader views of H5N1 evolution available as: | ||
| - [nextstrain.org/avian-flu/h5n1/ha/2y](https://nextstrain.org/avian-flu/h5n1/ha/2y) | ||
| - [nextstrain.org/avian-flu/h5n1/na/2y](https://nextstrain.org/avian-flu/h5n1/na/2y) | ||
| - etc... |
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