|
Genomes
|
Cand. C. ruddii PV
|
B. garinii Pbi
|
P. gingivalis W83
|
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.
