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Table 3  A comparison of the number of transcripts found and matched to a reference for the simulated reads (Mouse)

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

Assembler # of candidates found # of transcripts matched for Target coverage of
≥ 95% ≥ 90% ≥ 80%
SOAPdenovo-trans 21,640 4792 5730 6353
Trans-ABySS 29,642 5330 6280 6934
Trinity 27,962 5499 6314 7067
BinPacker 19,489 5117 5920 6655
Muli-k OASES 56,885 7201 8132 8727
Bridger 22,737 6015 6781 7378
TraRECo, Dth = 0.05, CDth = 0 42,275 7923 8739 9205
TraRECo, Dth = 0.05, CDth = 1 27,005 7700 8511 8975
TraRECo, Dth = 0.05, CDth = 2 26,398 7677 8481 8946
TraRECo, Dth = 0.05, CDth = 4 19,813 7613 8395 8840
TraRECo, Dth = 0.05, CDth = 6 15,540 7540 8298 8704
TraRECo, Dth = 0.05, CDth = 8 13,502 7420 8110 8451
TraRECo, Dth = 0.05, CDth = 12 11,503 6941 7473 7696
TraRECo, Dth = 0.05, CDth = 16 10,290 6408 6821 6997
The number of Transcripts generated with its expressed coverage ≥ Target coverage 9911 11,538 12,733
  1. Target coverage = 95%, 90% and 80%. For TraRECo, the results with Dth = 0.05 and CDth = 0, 1, 2, 4, 6, 8, 12 and 16 are shown