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Table 2  A comparison of the number of transcripts found and matched to a reference for the paired-end read data SRX062280 (Mouse sample)

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 48,234 4902 6088 7634
Trans-ABySS 70,052 8202 9673 11,680
Trinity 71,415 10,247 11,645 13,543
BinPacker 34,838 8979 10,151 11,685
Multi-k OASES 174,724 11,256 13,224 15,789
TraRECo, Dth = 0.06, CDth = 0 240,907 11,864 13,980 17,076
TraRECo, Dth = 0.06, CDth = 1 82,522 10,480 12,355 14,927
TraRECo, Dth = 0.06, CDth = 2 78,226 10,347 12,183 14,688
TraRECo, Dth = 0.06, CDth = 4 65,823 9978 11,706 14,080
TraRECo, Dth = 0.06, CDth = 6 52,465 9555 11,166 13,353
TraRECo, Dth = 0.06, CDth = 8 43,550 9146 10,638 12,643
TraRECo, Dth = 0.06, CDth = 12 33,704 8313 9614 11,282
TraRECo, Dth = 0.06, CDth = 16 28,132 7577 8708 10,087
  1. Except for Trinity, the cutadapt SW was used for read data trimming
  2. Target coverage = 95%, 90% and 80%. For TraRECo, the results with Dth = 0.06 and CDth = 0, 1, 2, 4, 6, 8, 12 and 16 are shown
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