Assembly Regression Testing

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.