Skip to main content

Table 4 A comparison of DETONATE (RSEM-EVAL) scores for the three data samples

From: TraRECo: a greedy approach based de novo transcriptome assembler with read error correction using consensus matrix

Assembler SRR445718 (Human) SRX062280 (Mouse) Simulated reads
SOAPdenovo-trans -1,714,875,885 −11,260,544,990 a −1,601,887,363
Trans-ABySS − 1,450,049,444 a − 11,304,600,611 − 1,528,116,522
Trinity − 1,489,443,203 − 11,327,881,219 − 1,482,875,599 a
BinPacker − 1,479,768,971 − 11,281,390,921 −1,620,059,120
Muli-k OASES −2,333,599,533 −11,623,498,121 −2,031,443,441
Bridger −1,479,768,971 Not available −1,540,527,574
TraRECo, CDth = 0 −1,604,604,900 −12,088,126,158 − 1559,358,185
TraRECo, CDth = 1 −1,401,116,205 − 11,421,827,023 −1,481,790,008
TraRECo, CDth = 2 −1,391,489,463 a − 11,402,670,499 −1,480,014,038 a
TraRECo, CDth = 4 −1,392,964,314 −11,372,430,684 − 1,486,956,413
TraRECo, CDth = 6 − 1,419,050,587 − 11,347,202,193 −1,506,415,171
TraRECo, CDth = 8 −1,452,606,806 − 11,327,444,550 −1,530,794,253
TraRECo, CDth = 12 −1,529,402,883 − 11,300,573,327 −1,581,922,133
TraRECo, CDth = 16 −1,598,153,693 − 11,282,292,195 a −1,630,265,385
  1. Best performance among benchmark assemblers and among TraRECo with different coverage depth thresholds were marked with a. For TraRECo, Dth = 0.05 was used for simulated read, while 0.06 for real reads