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Assembly Regression Testing

Compare old versus new Terra assembly outputs across matched samples.

198|67|Updated Sep 25, 2014
Search Tags:#regression testing#viral ngs#assembly comparison#mafft alignment#vadr#terra gcs
One-click install
npx skills add https://github.com/broadinstitute/viral-ngs --skill assembly-regression-testing
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Assembly Regression Testing
Source: https://github.com/broadinstitute/viral-ngs/tree/main/.agents/skills/regression-testing
Command: npx skills add https://github.com/broadinstitute/viral-ngs --skill assembly-regression-testing

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps you validate that changes to the assembly or variant-calling pipeline do not introduce unintended biological or technical differences by comparing old vs new outputs across real Terra samples.

Core Features & Use Cases

  • End-to-end regression comparison: Pairs assemblies produced by old and new code for the same samples and checks equivalence or improvement.
  • Metric + alignment divergence analysis: Downloads assembly statistics TSVs, aligns FASTAs with mafft, and quantifies SNPs, indels (events and bp), ambiguity diffs, and terminal extensions.
  • Multi-segment genome correctness: Aligns segments independently (by FASTA header when possible) to prevent boundary artifacts from being misclassified as internal indels.
  • Optional VADR quality assessment: Uses dsub to batch-run VADR on divergent assemblies (especially helpful when indels could cause frameshifts and downstream annotation issues).
  • Aggregated visual and markdown reporting: Produces plots and a summary markdown report suitable for PR comments.

Quick Start

Ask the Skill to run discovery, compare all paired samples, and generate the report by using the old and new Terra submission IDs you provide.

Frequently Asked Questions about Assembly Regression Testing

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run regression testing for viral genome assembly changes in Terra?▼

Run regression testing for viral genome assembly by pairing old and new Terra submission IDs to compare matched samples, quantify alignment divergence, and generate a markdown report for PR validation.

What's the best way to compare old and new assembly FASTA outputs across matched samples?▼

Compare old and new assembly FASTA outputs by aligning sequences with mafft, then quantifying SNPs, indels, ambiguity diffs, and terminal extensions to catch unintended pipeline regressions before release.

How does multi-segment viral genome alignment prevent indel boundary artifacts during assembly comparison?▼

Multi-segment viral genome alignment prevents boundary artifacts by aligning segments independently via FASTA headers, ensuring terminal extensions are not misclassified as internal indels during regression testing.

Do I need gcloud and dsub access to run VADR quality assessment on divergent assemblies?▼

You need gcloud access to Terra GCS buckets for downloading outputs and can use dsub to batch-run VADR quality assessment on divergent assemblies, especially to detect frameshifts from indels.

What metrics are aggregated when validating variant-calling pipeline changes?▼

Validating variant-calling pipeline changes aggregates assembly statistics TSVs, calculates pairwise alignment divergence metrics, and produces matplotlib plots alongside a summary markdown report suitable for PR comments.

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