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

Table 1 A comparison of the number of transcripts found and matched to a reference for the single-end reads SRR445718 (Human sample)

Assembler	# of candidates found	# of transcripts matched for Target coverage of
Assembler	# of candidates found	≥ 95%	≥ 90%	≥ 80%
SOAPdenovo-trans	48,462	2613	3522	5349
Trans-ABySS	87,686	3626	4781	6967
Trinity	82,865	4008	5279	7680
BinPacker	20,612	3486	4314	5685
Multi-k OASES	202,152	5120	6737	9520
Bridger	58,217	4013	5093	7017
TraRECo, D_th = 0.06, CD_th = 0	219,402	5366	7010	10,168
TraRECo, D_th = 0.06, CD_th = 1	118,342	4845	6308	9078
TraRECo, D_th = 0.06, CD_th = 2	109,551	4774	6209	8901
TraRECo, D_th = 0.06, CD_th = 4	79,073	4537	5890	8393
TraRECo, D_th = 0.06, CD_th = 6	58,396	4217	5436	7642
TraRECo, D_th = 0.06, CD_th = 8	47,095	3937	5026	6973
TraRECo, D_th = 0.06, CD_th = 12	35,506	3396	4305	5880
TraRECo, D_th = 0.06, CD_th = 16	28,997	2959	3749	5089

Except for Trinity, Cutadapt 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