Table 4 Running time in processor-hours, with the values to the left and to the right of “+” indicating the running time of Velvet and Oases respectively (or ABySS and Trans-ABySS respectively), organism indicating the related model organism, time indicating the running time of extVelvet (or extABySS), chosen indicating the number of nodes that are chosen for extension, de Bruijn indicating the number of nodes in the de Bruijn graph, and database indicating the number of transcripts in the database
Least stringent k_c | Organism | Time | Chosen | De Bruijn | Database |
|---|---|---|---|---|---|
S. pom (84+0.2) | S. pom | 45 | 41692 | 536894 | 5011 |
S. cer | 12 | 15252 | 536894 | 5907 | |
N. cra | 12 | 16366 | 536894 | 10082 | |
D. mel (6.7+4.4) | D. mel | 238 | 138972 | 459644 | 22102 |
D. pse | 67 | 64012 | 459644 | 16071 | |
A. gam | 32 | 41580 | 459644 | 12659 | |
H. sap (45+0.2) | H. sap | 595 | 222244 | 1133368 | 32787 |
S. bol | 490 | 88340 | 1133368 | 25621 | |
M. mus | 167 | 85166 | 1133368 | 29617 | |
A. tha (112+0.2) | A. tha | 2495 | 423410 | 3111862 | 41671 |
A. lyr | 944 | 218760 | 3111862 | 32549 | |
O. sat | 616 | 144058 | 3111862 | 26777 | |
L. ser (1.2+0.2) | D. mel | 67 | 41872 | 257700 | 22102 |
H. gla (368+0.2) | H. sap | 1920 | 192772 | 5457968 | 32799 |
C. soc (440+0.2) | H. sap | 1344 | 175690 | 5030586 | 32799 |
C. ari (4.2+4.6) | A. tha | 200 | 103524 | 1205362 | 41671 |
M. alb (5.8+2.9) | A. tha | 79 | 82996 | 562210 | 41671 |
M. sic (9.3+6.8) | A. tha | 67 | 83718 | 482826 | 41671 |