Table 4 Comparisons of the Drosophila transcriptome assemblies of our postprocessing algorithm, Oases and Trans-ABySS using four publicly available libraries over different values of k and k-mer coverage cutoff c. The notations are the same as in Table 3.
postprocess | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
k_c | initial nodes | largest tangle | largest SCC | splicing graphs | max length | N50 | >1-node graphs | max node | avg nodes | SNPs | total hits | unique hits | >1-hit graphs | max hits | time (mins) | memory (GB) |
31_3 | 293034 | 251819 | 132958 | 87306 | 7571 | 542 | 1914 | 36 | 5 | 13216 | 37135 | 10752 | 516 | 7 | 81,24 | 20,2 |
31_5 | 153123 | 115511 | 60504 | 53199 | 9708 | 748 | 1881 | 98 | 5 | 8419 | 27103 | 9868 | 683 | 8 | 81,23 | 20,2 |
31_10 | 70809 | 36861 | 19839 | 35955 | 7393 | 621 | 1224 | 108 | 5 | 3746 | 22037 | 8399 | 442 | 8 | 81,21 | 20,2 |
35_3 | 175184 | 123605 | 85923 | 73584 | 7525 | 559 | 2246 | 79 | 6 | 10311 | 37115 | 10565 | 737 | 8 | 81,22 | 20,2 |
35_5 | 98897 | 58409 | 40689 | 47081 | 9382 | 731 | 1808 | 134 | 6 | 6741 | 26560 | 9631 | 743 | 12 | 81,21 | 20,2 |
35_10 | 48595 | 19438 | 13375 | 28269 | 7008 | 706 | 1062 | 90 | 5 | 2967 | 17829 | 7883 | 461 | 8 | 81,19 | 20,2 |
Oases | ||||||||||||||||
k _c | locus | max length | N50 | >1-trans locus | max trans | avg trans | total hits | unique hits | >1-hit locus | max hits | time (mins) | memory (GB) | ||||
31_3 | 35587 | 15986 | 994 | 4881 | 18 | 3 | 26559 | 10819 | 410 | 5 | 87,24 | 25,27 | ||||
31_5 | 26679 | 15906 | 1109 | 3234 | 20 | 3 | 21084 | 9944 | 336 | 5 | 87,21 | 25,21 | ||||
31_10 | 21283 | 8174 | 877 | 1637 | 16 | 3 | 17225 | 8449 | 188 | 4 | 87,19 | 25,21 | ||||
35_3 | 37377 | 9826 | 846 | 3724 | 16 | 3 | 28492 | 10652 | 346 | 6 | 75,14 | 17,17 | ||||
35_5 | 27573 | 12562 | 979 | 2644 | 14 | 3 | 21992 | 9751 | 332 | 5 | 75,13 | 17,17 | ||||
35_10 | 18072 | 7934 | 939 | 1389 | 12 | 3 | 14614 | 7953 | 194 | 5 | 75,12 | 17,17 | ||||
Trans-ABySS | ||||||||||||||||
k _c | trans | max length | N50 | >1-node trans | max nodes | avg nodes | total hits | unique hits | time (mins) | memory (GB) | ||||||
31_3 | 113157 | 14353 | 1149 | 72266 | 56 | 6 | 33780 | 10527 | 201,1 | 4,1 | ||||||
31_5 | 62292 | 14395 | 1282 | 37656 | 72 | 6 | 24614 | 9810 | 193,1 | 4,1 | ||||||
31_10 | 32509 | 17057 | 1075 | 19837 | 50 | 5 | 16676 | 8313 | 172,1 | 4,1 | ||||||
35_3 | 76220 | 14351 | 1142 | 40606 | 79 | 6 | 31619 | 10288 | 179,1 | 4,1 | ||||||
35_5 | 46431 | 14385 | 1239 | 23632 | 38 | 5 | 23451 | 9603 | 172,1 | 4,1 | ||||||
35_10 | 24956 | 9139 | 1095 | 12968 | 30 | 5 | 15057 | 7956 | 154,1 | 4,1 | ||||||