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December 22, 2021 00:14
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Example Nextstrain builds definition for seasonal flu
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| # Define lineages for the analysis. | |
| lineages: | |
| - h3n2 | |
| - h1n1pdm | |
| - vic | |
| - yam | |
| # Define genes to translate from nucleotide to amino acid sequences. These names | |
| # must match coding regions defined in the reference. | |
| genes: | |
| - SigPep | |
| - HA1 | |
| - HA2 | |
| # Define parameters for specific steps of the workflow by name. | |
| download_sequences: | |
| database: vdb | |
| virus: flu | |
| segment: ha | |
| fasta_fields: strain virus accession collection_date region country division location passage_category submitting_lab age gender | |
| resolve_method: split_passage | |
| download_titers: | |
| databases: cdc_tdb vidrl_tdb tdb | |
| virus: flu | |
| select: assay_type:hi serum_passage_category:cell | |
| filter_titers: | |
| exclude: niid | |
| parse: | |
| fasta_fields: strain virus isolate_id date region country division location passage authors age gender | |
| subsample: | |
| # Omit test strains that have egg passage annotated in their names. This can | |
| # happen even if the passage type is not set to 'egg'. | |
| query: "~strain.str.contains('egg')" | |
| # Exclude low-quality strains (missing key metadata) or those passaged through | |
| # eggs. | |
| exclude_where: country=? region=? passage=egg | |
| # For optimal date inference of internal nodes by TreeTime, omit strains with | |
| # date ambiguity at the month or year resolution. | |
| exclude_ambiguous_dates_by: month | |
| min_date: 2010-01-01 | |
| max_date: 2020-01-01 | |
| min_length: 900 | |
| # Evenly sample strains across major geographic regions (e.g., Southeast Asia, | |
| # Europe, North America, etc.) and time. | |
| group_by: region year month | |
| subsample_max_sequences: 3000 | |
| filter: | |
| # Allow earlier strains that were included as references in the initial | |
| # subsampling. | |
| min_date: 2009-01-01 | |
| max_date: 2020-01-01 | |
| refine: | |
| coalescent: const | |
| date_inference: marginal | |
| clock_filter_iqd: 4 | |
| clock_rate: 0.0043 | |
| clock_std_dev: 0.00086 | |
| ancestral: | |
| inference: joint | |
| export: | |
| color_by_metadata: country region | |
| frequencies: | |
| narrow_bandwidth: 0.1667 | |
| proportion_wide: 0.0 | |
| min_date: 2010-01-01 | |
| max_date: 2020-01-01 | |
| pivot_interval: 1 |
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