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pathogen-variant-surveillance

Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence has moved week to week. Triggers include "variant surveillance", "genomic surveillance", "what variant is circulating", "dominant variant", "Pango lineage", "lineage prevalence", "growth advantage", "SARS-CoV-2 variant", "XFG", "clade 2.3.4.4b", "H5N1 genotype", "influenza clade", "RSV/mpox/measles/dengue lineage", "CoV-Spectrum", "LAPIS", "Nextclade", "pango-designation", and any request to report what a pathogen population looks like today.

74

Quality

93%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

The canonical home for this skill is pathogen-variant-surveillance in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

86%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A strong, high-signal body: copy-paste-ready commands with real outputs, an unusually valuable traps table of verified API pitfalls, explicit validation gates (exit-code gating, incomplete-week flags, run-lag-first precedence), and a clean one-level reference structure that was verified to match the actual bundle. The only slack is illustrative output verbosity and time-stamped example data that is not quarantined from the evergreen guidance.

Suggestions

Trim or abridge the sample output tables (e.g., reporting_lag and mutation_profile) to the rows that teach something, and cut the prose justifying design choices such as the whole-ISO-week widening — the behavior statement alone suffices.

Move date-stamped material ("All verified against the live API on 2026-07-27" and dated example rows) into a short versioned/verification note so evergreen guidance stays separable from time-sensitive claims.

Add one explicit recovery instruction for the name-check gate — e.g., 'if resolve_lineage exits 1, replace withdrawn names with their redesignated successor before continuing' — to close the error-feedback loop the workflow otherwise implies.

DimensionReasoningScore

Conciseness

The body is dense and domain-specific — the traps table, per-instance field-name caveats, and the "never from memory" rule are all non-obvious information Claude does not already know, and there is no explanation of generic concepts. It falls at 4 rather than 5 because a few passages are illustrative rather than instructional: full sample output tables (e.g., the reporting_lag output and the four-row mutation table) and prose justifying design decisions ("A window starting mid-week would give a first row covering three days...") could be trimmed, and embedded time-sensitive details ("verified against the live API on 2026-07-27", dated example rows) are not quarantined in a versioned/deprecated section.

4 / 5

Actionability

Every section gives a copy-paste-ready command with real flags: `python3 lineage_prevalence.py --top 5 --where country=USA --weeks 12`, `resolve_lineage.py XFG.23.1.3 PQ.17 PC.2 NOTALINEAGE`, `mutation_profile.py "XFJ*" --versus "XFG*" --gene S --since 2026-01-01`, plus documented output format, `--format table|tsv|json`, and stderr/stdout provenance separation. The examples cover the common cases (discovery, name checking, growth, assay match, lag) — matching the fully-executable 5 anchor.

5 / 5

Workflow Clarity

The sections form a coherent ordered workflow with explicit checkpoints: "Start from the data, not from a remembered list" is labeled the right first command, resolve_lineage's exit code 1 "gates a manuscript's lineage list", incomplete weeks are flagged and excluded unless overridden, and "Run this **before** quoting any recent prevalence" states the lag-check precedence explicitly. It sits at 4 rather than 5 because the ordering lives mostly in section arrangement rather than a stated sequence, and there is no explicit error-recovery loop (e.g., what to do when a name resolves as withdrawn mid-analysis, beyond the PC.2 example).

4 / 5

Progressive Disclosure

SKILL.md is a genuine overview: the four scripts are summarized in a table, full trap detail is deferred with "full detail in `references/lapis-api.md`", and a References section lists all three reference files (lapis-api.md, lineage-nomenclature.md, surveillance-caveats.md — verified present) one level deep, each with a clear scope description. Content is appropriately split and navigation is easy, matching the 5 anchor.

5 / 5

Total

18

/

20

Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

An exemplary description: concrete third-person capability statement, explicit 'Use whenever...' trigger guidance with an extensive natural-language trigger list, and a sharply defined niche that distinguishes live-population queries from remembered knowledge. It is long, but every clause carries capability or trigger information rather than padding.

DimensionReasoningScore

Specificity

The description lists multiple concrete, comprehensive actions: "Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry", plus resolving Pango designations, identifying H5N1 clades/genotypes, and checking PCR primer/assay target matches. It stays in third person ("Query...", "find...") with no vague filler. This matches the 5 anchor (multiple specific concrete actions, comprehensive); it is above 4 because coverage is complete for the skill's scope rather than having minor gaps.

5 / 5

Completeness

It explicitly answers what ("Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry") and when ("Use whenever a question depends on the current state of a pathogen population rather than on remembered facts" followed by a concrete enumeration and an explicit "Triggers include..." clause). This is the 5 anchor verbatim in structure; the 'when' clause is explicit, not merely present.

5 / 5

Trigger Term Quality

The trigger list is exhaustive and natural: "variant surveillance", "what variant is circulating", "dominant variant", "Pango lineage", "lineage prevalence", "growth advantage", "XFG", "clade 2.3.4.4b", "H5N1 genotype", "influenza clade", "CoV-Spectrum", "LAPIS", "Nextclade", "pango-designation", plus a catch-all phrase "any request to report what a pathogen population looks like today". Both lay phrasing a user would naturally say and technical synonyms are present, matching the comprehensive 5 anchor; nothing common is missing.

5 / 5

Distinctiveness Conflict Risk

The niche is unambiguous — live pathogen population queries against LAPIS with pathogen-specific triggers ("Pango lineage", "H5N1 genotype", "clade 2.3.4.4b") — and the scope limiter "depends on the current state of a pathogen population rather than on remembered facts" keeps it from firing on ordinary static knowledge questions. Minimal overlap risk with adjacent bioinformatics skills; matches the 5 anchor (clear niche, distinct triggers).

5 / 5

Total

20

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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