Table 2 Runtime and maximum main memory usage for the construction of the compressed de Bruijn graph
From: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
k | Algorithm | 40 E. coli | 62 E. coli | 7 × Chr1 | 7 × HG |
|---|---|---|---|---|---|
init | SplitMEM | 117 (315.25) | 141 (317.00) | − | − |
init | A1, A2 | 38 (5.00) | 64 (5.00) | 380 (5.00) | − |
init | A3, A4 | 131 (1.32) | 202 (1.24) | 1168 (1.24) | 20,341 (1.24) |
50 | SplitMEM | 2261 (572.19) | − | − | − |
50 | A1 | 57 (5.22) | 92 (5.34) | 596 (6.20) | − |
50 | A2 | 61 (8.49) | 97 (8.78) | 619 (9.98) | − |
50 | A3 | 188 (2.23) | 300 (2.26) | 1733 (3.07) | 29,816 (2.77) |
50 | A3compr1 | 208 (1.81) | 346 (1.85) | 1880 (2.66) | 31,472 (2.36) |
50 | A3compr2 | 236 (1.63) | 374 (1.66) | 2318 (2.51) | 39,366 (2.22) |
50 | A4 | 164 (1.75) | 254 (1.82) | 1419 (1.28) | 25,574 (1.96) |
50 | A4compr1 | 167 (1.46) | 257 (1.53) | 1435 (1.28) | 25,866 (1.66) |
50 | A4compr2 | 179 (1.32) | 272 (1.24) | 1526 (1.24) | 27,365 (1.39) |
50 | A4+explicit | 172 (3.26) | 268 (3.35) | 1515 (3.59) | 27,619 (3.88) |
50 | A4compr1+explicit | 176 (2.97) | 271 (3.06) | 1541 (3.31) | 28,044 (3.64) |
50 | A4compr2+explicit | 188 (2.66) | 289 (2.74) | 1629 (2.96) | 29,517 (3.38) |
100 | SplitMEM | 2568 (572.20) | − | − | − |
100 | A1 | 59 (5.00) | 95 (5.00) | 595 (5.95) | − |
100 | A2 | 62 (7.89) | 99 (8.19) | 605 (9.74) | − |
100 | A3 | 188 (1.63) | 299 (1.68) | 1738 (2.74) | 27,815 (2.23) |
100 | A3compr1 | 205 (1.50) | 326 (1.49) | 1839 (2.33) | 30,401 (1.80) |
100 | A3compr2 | 232 (1.32) | 411 (1.29) | 2340 (2.14) | 38,134 (1.66) |
100 | A4 | 174 (1.71) | 261 (1.79) | 1422 (1.28) | 25,723 (1.94) |
100 | A4compr1 | 171 (1.42) | 264 (1.50) | 1439 (1.28) | 26,040 (1.64) |
100 | A4compr2 | 185 (1.32) | 289 (1.24) | 1544 (1.24) | 27,464 (1.37) |
100 | A4+explicit | 178 (2.61) | 270 (2.73) | 1486 (3.21) | 26,878 (3.36) |
100 | A4compr1+explicit | 175 (2.32) | 273 (2.44) | 1500 (2.92) | 26,999 (3.07) |
100 | A4compr2+explicit | 190 (2.01) | 299 (2.12) | 1624 (2.68) | 28,665 (2.80) |
500 | SplitMEM | 2116 (570.84) | − | − | − |
500 | A1 | 72 (5.00) | 113 (5.00) | 620 (5.83) | − |
500 | A2 | 83 (7.17) | 117 (7.43) | 640 (9.66) | − |
500 | A3 | 194 (1.50) | 304 (1.49) | 1752 (2.67) | 28,548 (2.07) |
500 | A3compr1 | 216 (1.50) | 325 (1.49) | 1839 (2.19) | 30,488 (1.65) |
500 | A3compr2 | 241 (1.32) | 378 (1.29) | 2319 (2.06) | 36,993 (1.50) |
500 | A4 | 184 (1.65) | 283 (1.74) | 1453 (1.28) | 26,362 (1.93) |
500 | A4compr1 | 197 (1.35) | 287 (1.44) | 1477 (1.28) | 26,545 (1.63) |
500 | A4compr2 | 213 (1.32) | 322 (1.24) | 1622 (1.24) | 28,501 (1.36) |
500 | A4+explicit | 185 (1.81) | 285 (1.90) | 1509 (3.14) | 27,285 (3.14) |
500 | A4compr1+explicit | 198 (1.52) | 288 (1.61) | 1535 (2.83) | 27,417 (2.79) |
500 | A4compr2+explicit | 214 (1.32) | 323 (1.29) | 1694 (2.56) | 29,283 (2.58) |