Benchmark datasets

Tiered approach

Dragon is benchmarked at three scales to validate scalability from laptop to server:

Tier 1: Small (development & CI)

Property	Value
Genomes	500 complete E. coli / Shigella from RefSeq
Total sequence	~2.5 Gbp
Redundancy	High (~95% ANI within species)
Index time	<1 hour
Index size	~1.5 GB
Use case	Unit testing, CI, rapid iteration

Tier 2: Medium (validation)

Property	Value
Genomes	~85,000 GTDB r220 representative genomes
Total sequence	~250 Gbp
Redundancy	Medium (one genome per species)
Index time	~1 hour
Index size	~15 GB
Use case	Sensitivity/accuracy validation

Tier 3: Large (full benchmark)

Property	Value
Genomes	~2.34M GenBank + RefSeq prokaryotic assemblies
Total sequence	~10 Tbp
Redundancy	Very high (many strains per species)
Index time	~12 hours
Index size	~100 GB
Use case	Full-scale comparison with LexicMap

Query types

Gene-level queries (primary)

• 1,000 random subsequences (500-5,000 bp) extracted from 100 diverse genomes

• Controlled mutations at 6 divergence levels: 0%, 1%, 3%, 5%, 10%, 15%

• Mutation model: 70% substitutions, 20% insertions, 10% deletions

Long reads (Badread)

• Simulated Oxford Nanopore reads from 50 genomes

• Mean length: 5 Kbp

• Identity range: 85-99%

• Chimera rate: 1%

Challenging scenarios

• 16S rRNA: highly conserved, extreme seed frequency

• Plasmids: 10-200 Kbp, multi-copy

• AMR genes: batch of 1,003 genes from CARD database

• HGT events: genes implanted from distant species