Table 2.
Comparisons of transcriptome assemblies of SOAPdenovo-Trans, Trans-ABySS and ASplice in model organisms over different values of k and k-mer coverage cutoff c
| S. pom | SOAPdenovo-Trans | Trans-ABySS | ASplice | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| total | unique | mem | total | unique | mem | splicing | total | unique | mem | ||||||
| k_c | locus | N50 | hits | hits | (GB) | trans | N50 | hits | hits | (GB) | graphs | N50 | hits | hits | (GB) |
| 25_10 | 3267 | 4455 | 7343 | 4230 | 10 | 21215 | 2854 | 28376 | 4400 | 3 | 5859 | 3032 | 5271 | 4650 | 9 |
| 25_20 | 3393 | 3795 | 7153 | 4341 | 10 | 14193 | 2880 | 19541 | 4284 | 3 | 5231 | 2723 | 4941 | 4579 | 9 |
| 25_50 | 3747 | 3025 | 8174 | 4513 | 10 | 8748 | 2317 | 10686 | 4370 | 3 | 5163 | 2210 | 5002 | 4580 | 9 |
| 31_10 | 3366 | 4164 | 8481 | 4342 | 10 | 20569 | 2977 | 33192 | 4323 | 4 | 5580 | 3005 | 5148 | 4611 | 9 |
| 31_20 | 3470 | 3590 | 7864 | 4418 | 10 | 13701 | 3045 | 22303 | 4158 | 4 | 5076 | 2625 | 4956 | 4565 | 9 |
| 31_50 | 3891 | 2788 | 8783 | 4576 | 10 | 7972 | 2421 | 10259 | 4284 | 4 | 5103 | 2088 | 5080 | 4620 | 9 |
| A. tha | SOAPdenovo-Trans | Trans-ABySS | ASplice | ||||||||||||
| total | unique | mem | total | unique | mem | splicing | total | unique | mem | ||||||
| k_c | locus | N50 | hits | hits | (GB) | trans | N50 | hits | hits | (GB) | graphs | N50 | hits | hits | (GB) |
| 25_10 | 18980 | 1705 | 80644 | 21614 | 17 | 348069 | 460 | 383663 | 21715 | 7 | 103450 | 344 | 92605 | 21487 | 10 |
| 25_20 | 16327 | 1622 | 71684 | 20239 | 17 | 159952 | 772 | 139875 | 20213 | 7 | 71419 | 561 | 66645 | 20033 | 9 |
| 25_50 | 13384 | 1472 | 53209 | 17788 | 17 | 66058 | 948 | 70136 | 17544 | 7 | 43407 | 778 | 42396 | 17535 | 9 |
| 31_10 | 19604 | 1700 | 74854 | 20952 | 17 | 350165 | 578 | 525359 | 21422 | 7 | 92665 | 444 | 88408 | 21288 | 10 |
| 31_20 | 16882 | 1605 | 62748 | 19516 | 17 | 141642 | 948 | 181322 | 19838 | 7 | 58877 | 760 | 56869 | 19691 | 9 |
| 31_50 | 13660 | 1438 | 42763 | 16990 | 17 | 54189 | 1083 | 75863 | 17050 | 7 | 35448 | 973 | 34906 | 17030 | 9 |
| D. mel | Trans-ABySS | ASplice | |||||||||||||
| total | unique | mem | splicing | total | unique | mem | |||||||||
| k_c | trans | N50 | hits | hits | (GB) | graphs | N50 | hits | hits | (GB) | |||||
| 25_10 | 135048 | 1192 | 179499 | 12989 | 27 | 99930 | 728 | 51854 | 12322 | 11 | |||||
| 25_20 | 83303 | 1693 | 102591 | 12848 | 27 | 60662 | 1328 | 35402 | 12245 | 10 | |||||
| 25_50 | 47341 | 2082 | 58523 | 12453 | 27 | 36093 | 1874 | 26130 | 11921 | 9 | |||||
| 31_10 | 113805 | 1547 | 225887 | 13025 | 30 | 77439 | 1203 | 45278 | 12453 | 11 | |||||
| 31_20 | 70061 | 2029 | 124050 | 12787 | 30 | 45645 | 1952 | 28616 | 12259 | 10 | |||||
| 31_50 | 41210 | 2296 | 64736 | 12337 | 30 | 32593 | 2085 | 24093 | 11861 | 9 | |||||
The predicted units are locus for SOAPdenovo-Trans that is represented as a splicing graph containing nodes and edges, transcript (trans) for Trans-ABySS that is a linear concatenation of constituent nodes, and splicing graph for ASplice. For SOAPdenovo-Trans and ASplice, N50 denotes the N50 value of the length (in nucleotides) of the longest path in each splicing graph. For Trans-ABySS, N50 denotes the N50 value of the length of a predicted transcript, and only predicted transcripts of length at least 100 are retained. Total hits denotes the total number of hits from nucleotide BLAST search of nodes to the transcriptome of the same organism. Isoforms are considered to be the same gene. Only the top hit with E-value below 10−7 is considered. Hits from nodes within the same predicted unit to the same gene are counted only once. Unique hits denotes the number of unique hits to different genes. Mem (GB) denotes the physical memory requirement in gigabytes over all stages of each algorithm