I assembled an animal transcriptome de novo using strand-specific paired-end Illumina sequence data and the Oases/velvet software package (supporting strand specific data). Using the same sequence data, I also assembled a transcriptome using CLC software (CLC genomic workbench, not supporting strand-specific data for de novo assembly). Comparing these two transcriptomes (Oases vs CLC) for several reference genes (> 50) revealed that the CLC assembly was much better than the Oases version (e.g. in the CLC transcriptome genes were not fragmented into several contigs and a larger number of full length genes were assembled with CLC).
I understand strand-specific sequence data is very useful for measuring strand-specific expression but is it also favourable to use strand-specific information when assembling a transcriptome. A literature search couldn't make me much wiser....