Amplicon primer-start assignment: ARTIC V3 public lane

• Category: Public data

• Assay type: amplicon_panel

• Evidence level: Documented example

• Dataset: nf-core viralrecon ARTIC V3 Illumina R1 sample

• Condition shown: Fixed-window primer-start assignment with exact-prefix baseline agreement.

• Primary report: docs/benchmarks/amplicon_panel/README.md

What This Shows

• DotMatch can report fixed-window known-primer assignment on a public amplicon-style read lane.

• Ambiguity handling is checked separately from downstream consensus or variant calling.

What It Does Not Show

• This is not primer trimming.

• Consensus generation, variant calling, clinical panels, and diagnostic interpretation are outside this evidence lane.

Comparator And Validation

Comparator semantics: The public lane uses nf-core/test-datasets viralrecon Illumina ARTIC V3 R1, ARTIC V3 primer targets, and a transparent exact-prefix baseline.

Validation: The public gate requires synthetic diagnostics, public DotMatch k=0 and k=1 rows, zero validation mismatches, exact agreement with the k=0 baseline, and k=1 assignment count no lower than k=0.

Report Examples

• Amplicon/panel benchmark report (markdown)

Raw Artifacts

• benchmarks/raw/amplicon_panel.csv

• examples/amplicon_panel/data/metadata.json

Reproduce Or Check

• make bench-amplicon-panel-public

• make amplicon-panel-public-gate