Table 1.

Number of Transcripts Produced by the Individual Assembly Programs and Their Contribution to the Final Transcriptome

Assembler	Total contigs	Contigs after CD-HIT-EST	Transcripts in okay-main set	Transcripts in alternative set
Trinity	100,749	100,749	9,848	5,251
Trans-ABySS	185,991	185,991	4,962	13,729
Oases-Velvet	442,560	126,055	9,692	19,225
SOAPdenovo	489,649	170,562	8,401	9,644
Total	1,218,949	583,357	32,903	47,849