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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