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

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

Assembler	# of candidates found	# of transcripts matched for Target coverage of
Assembler	# of candidates found	≥ 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, D_th = 0.06, CD_th = 0	240,907	11,864	13,980	17,076
TraRECo, D_th = 0.06, CD_th = 1	82,522	10,480	12,355	14,927
TraRECo, D_th = 0.06, CD_th = 2	78,226	10,347	12,183	14,688
TraRECo, D_th = 0.06, CD_th = 4	65,823	9978	11,706	14,080
TraRECo, D_th = 0.06, CD_th = 6	52,465	9555	11,166	13,353
TraRECo, D_th = 0.06, CD_th = 8	43,550	9146	10,638	12,643
TraRECo, D_th = 0.06, CD_th = 12	33,704	8313	9614	11,282
TraRECo, D_th = 0.06, CD_th = 16	28,132	7577	8708	10,087

Except for Trinity, the cutadapt SW was used for read data trimming
Target coverage = 95%, 90% and 80%. For TraRECo, the results with D_th = 0.06 and CD_th = 0, 1, 2, 4, 6, 8, 12 and 16 are shown

ISSN: 1471-2164