Table 2.

Pipeline run time for different probe design sets

Genomes	Cand.C. ruddii PV	B. garinii Pbi	P. gingivalisW83	E. coli K12 MG1655	S. cellulosum 'So ce 56'
Genome size	~0.16 Mbp	~1.22 Mbp	~2.34 Mbp	~4.6 Mbp	~13 Mbp
Characteristic	Small	Multiple	Oral pathogen	E. coli	Large
Probe number (NG format)	72 K (4*72 K)	192.5 K (385 K/2)	385 K	770 K (2*385 K)	1620 K (12*135 K)
Probe size	50	50	50	50	50
Min. probe size	45	45	45	45	48
Run time
Step 1	<1 min	<2 min	2 min	6 min	16 min
Step 2	<1 min	8 min	16 min	31 min	1 h 3 min
Step 3 (blastn, -W 7)*	12 min	1 h 43 min	2 h 57 min	6 h 37 min	76 h
Step 4 (hybrid-ss-min)*	6 min	43 min	69 min	2 h 25 min	8 h
Step 5,6	<1 min	7 min	6 min	11 min	31 min
Total run time	~15 min	~2 h	~3 h 21 min	~7 h 25 min	~77 h 50 min

*Run in parallel, only most time consuming step is included in the total run time. Word size 7 is used for blastn.