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broadinstitutebroadinstituteOfficial·4 Agent Skills Included

viral-ngs

Viral genome sequencing analysis, assembly, and classification

Analyzes viral next-generation sequencing data, from raw read processing to genome assembly, metagenomic classification, and variant calling. Removes the burden of manually wiring together dozens of bioinformatics tools like Kraken2, SPAdes, and samtools. Ships pre-built Docker images and regression-testing playbooks so research teams get reproducible results faster.
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npx skills add broadinstitute/viral-ngs --all -g -y
Available:

Tells your AI agent how the viral-ngs codebase is structured, how to run tests inside Docker containers, and the rules for adding new bioinformatics tool wrappers.

All Skills in This Repository (4)

Pure Emerald Level Indicators
📦 In Repo
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Assembly Regression Testing

Compare old versus new Terra assembly outputs across matched samples.

Official
Advanced
📦 In Repo
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Claude on Vertex AI from GitHub Actions

Invoke Claude on Google Vertex AI from GitHub Actions workflows.

Official
Intermediate
📦 In Repo
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Container Vulnerability Management

Scan viral-ngs Docker images with Trivy and triage HIGH/CRITICAL CVEs.

Official
Advanced
📦 In Repo
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Running Batch Jobs on GCP via dsub

Batch-execute containerized viral genomics workloads on Google Cloud with dsub.

Official
Intermediate

Frequently Asked Questions

FAQPage Schema
How to install viral-ngs?▼

Run `npx skills add broadinstitute/viral-ngs --all -g -y` in your terminal to install all skills in this suite globally.

What does viral-ngs do?▼

It is a collection of command-line tools for viral genome sequencing analysis, covering read processing, genome assembly, metagenomic classification, and variant calling.

How do I run viral-ngs without installing bioinformatics tools?▼

Use the pre-built Docker images from Quay.io, which bundle all dependencies like samtools, Kraken2, and SPAdes so you can run analyses with a single docker command.

Can viral-ngs compare pipeline outputs across code versions?▼

Yes. The regression-testing skill compares old and new assembly outputs across hundreds of samples, aligns genomes, and generates reports highlighting SNP and indel differences.

Does viral-ngs work on Apple Silicon?▼

Yes. Docker images are built for both amd64 and arm64, though a few x86-only tools are skipped on ARM builds.

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