Performance tuning

Hardware recommendations

Component	Minimum	Recommended	Notes
RAM (query)	4 GB	8 GB	Dragon stays <4 GB; extra for OS
RAM (index build)	8 GB	32-64 GB	SA-IS construction
Storage	SSD	NVMe SSD	Memory-mapped access; HDD 5-10x slower
CPU	2 cores	8+ cores	Parallel queries via rayon

SSD vs HDD

Dragon’s index is memory-mapped, so I/O speed directly affects performance:

Storage	Single gene query	Batch (1000 genes)
NVMe SSD	~1 second	~5 minutes
SATA SSD	~3 seconds	~15 minutes
HDD	~15 seconds	~2 hours

Recommendation: use SSD whenever possible. If using HDD, increase --max-ram to keep more index pages resident.

Tuning parameters

For maximum sensitivity

dragon search \
  --min-seed-len 12 \
  --max-seed-freq 50000 \
  --min-chain-score 20 \
  --max-target-seqs 500

For maximum speed

dragon search \
  --min-seed-len 21 \
  --max-seed-freq 1000 \
  --min-chain-score 100 \
  --max-target-seqs 10 \
  --threads 16

For low-memory machines (4 GB total RAM)

dragon search \
  --max-ram 2.0 \
  --threads 2

Scaling guidelines

Number of genomes vs resources

Genomes	Index disk	Query RAM	Build time
100	200 MB	<500 MB	5 seconds
1,000	1 GB	<500 MB	30 seconds
10,000	5 GB	1 GB	10 minutes
100,000	20 GB	2 GB	2 hours
1,000,000	60 GB	3 GB	8 hours
2,340,000	100 GB	3.5 GB	12 hours

Query length vs performance

Query length	Seeds found	Chaining time	Total time
150 bp	~5	<1 ms	~0.1 s
1,000 bp	~30	~5 ms	~0.5 s
10,000 bp	~300	~50 ms	~2 s
100,000 bp	~3,000	~500 ms	~15 s

Distributing pre-built indices

Since index construction is expensive but only done once, consider:

Build once on a server with sufficient RAM
Distribute the index to query machines (e.g., via rsync, S3, or shared filesystem)
Query on laptops with just 4 GB RAM

# On build server
dragon index -i all_genomes/ -o dragon_index/ -j 32

# Transfer to query machine
rsync -avP dragon_index/ user@laptop:~/dragon_index/

# On laptop
dragon search -i ~/dragon_index/ -q my_query.fa -o results.paf