pathogen-variant-surveillance
Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage.
- Version
- 1.3
- License
- MIT
- Compatibility
- Requires Python 3.11+. Scripts use only the standard library. Needs network access to public LAPIS deployments on lapis.cov-spectrum.org, lapis.genspectrum.org, lapis.pathoplexus.org and raw.githubusercontent.com for pango-designation. No credentials for these public queries.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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Files
- skills/pathogen-variant-surveillance/SKILL.md
- skills/pathogen-variant-surveillance/SKILL_CN.md
- skills/pathogen-variant-surveillance/references/lapis-api.md
- skills/pathogen-variant-surveillance/references/lineage-nomenclature.md
- skills/pathogen-variant-surveillance/references/surveillance-caveats.md
- skills/pathogen-variant-surveillance/scripts/lapis_client.py
- skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py
- skills/pathogen-variant-surveillance/scripts/mutation_profile.py
- skills/pathogen-variant-surveillance/scripts/reporting_lag.py
- skills/pathogen-variant-surveillance/scripts/resolve_lineage.py
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