Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-epidemiological-genomics-variant-surveillance

Maintainer FreedomIntelligence · Last updated April 1, 2026

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

OpenClawNanoClawAnalysisReproductionbio-epidemiological-genomics-variant-surveillance🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epidemiological & causal genomicsassign

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epidemiological-genomics-variant-surveillance

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: nextclade run -d sars-cov-2 -i sequences.fasta.
CLI: pangolin sequences.fasta for SARS-CoV-2 Pango lineage assignment.
Classify my viral sequences into lineages" → Assign pathogen lineages and track variants of concern using Nextclade or pangolin for real-time genomic surveillance. CLI: nextclade run -d sars-cov-2 -i sequences.fasta CLI: pangolin sequences.fasta for SARS-CoV-2 Pango lineage assignment.
npm install -g @nextstrain/nextclade.

Source Doc

Excerpt From SKILL.md

Or download binary

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o nextclade chmod +x nextclade

Download dataset (e.g., SARS-CoV-2)

nextclade dataset get --name sars-cov-2 --output-dir data/sars-cov-2

Run analysis

nextclade run
--input-dataset data/sars-cov-2
--output-tsv results.tsv
--output-json results.json
sequences.fasta

Use cases

Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

epidemiological-genomics/phylodynamics - Time-scaled analysis of variants
variant-calling/variant-annotation - Mutation annotation
data-visualization/ggplot2-fundamentals - Visualize variant dynamics

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