Table 1.
Evaluation using a RNA-Seq dataset of 55 M paired-end 45-bp reads of human T cells
| Method | Original | SEECER | Quake | SEED | Coral | HiTEC | Echo |
|---|---|---|---|---|---|---|---|
| Aligned reads (M) | 31.2 | 33.8 (+8.4%) | 32.3(+3.6%) | – | 32.6 (+4.5%) | 31.2 (+0.0%) | 31.6 (+1.3%) |
| Proper read pairs (M) | 22.1 | 25.5 (+15.1%) | 23.4 (+5.8%) | – | 24.0 (+8.7%) | 22.1 (−0.0%) | 22.7 (+2.5%) |
| Zero error reads (M) | 18.3 | 27.3 (+49.6%) | 22 (+20.4%) | – | 23.9 (+30.7%) | 18.3 (0.1%) | 19.6 (+7.2%) |
| Gain | – | 0.56 | 0.25 | – | 0.38 | 0.00 | 0.024 |
| Assembly full length | 1749 | 2120 (+21%) | 1979 (+13%) | 1358 (−22%) | 2092 (+19.6%) | 1713 (−2.7%) | 1916 (+9.6%) |
| Assembly 80% length | 13 852 | 14 833 (+7%) | 14 267 (+3%) | 9686 (−30%) | 14 643 (+5.7%) | 13450 (−2.9%) | 14 273 (+3.0%) |
| Memory (GB) | – | 27 | 32 | – | 34.3 | 49 | 72 |
| Time (hours) | – | 12.25 | 7.25 | – | 2.42 | 6.33 | 13.7 |
Percentages in brackets denote performance compared with original data.
‘–’ means not applicable.
The evaluation is based on Ensembl 65 annotation.