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

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

Assembler	# of candidates found	# of transcripts matched for Target coverage of
Assembler	# of candidates found	≥ 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, D_th = 0.05, CD_th = 0	42,275	7923	8739	9205
TraRECo, D_th = 0.05, CD_th = 1	27,005	7700	8511	8975
TraRECo, D_th = 0.05, CD_th = 2	26,398	7677	8481	8946
TraRECo, D_th = 0.05, CD_th = 4	19,813	7613	8395	8840
TraRECo, D_th = 0.05, CD_th = 6	15,540	7540	8298	8704
TraRECo, D_th = 0.05, CD_th = 8	13,502	7420	8110	8451
TraRECo, D_th = 0.05, CD_th = 12	11,503	6941	7473	7696
TraRECo, D_th = 0.05, CD_th = 16	10,290	6408	6821	6997
The number of Transcripts generated with its expressed coverage ≥ Target coverage		9911	11,538	12,733

Target coverage = 95%, 90% and 80%. For TraRECo, the results with D_th = 0.05 and CD_th = 0, 1, 2, 4, 6, 8, 12 and 16 are shown

ISSN: 1471-2164