TransRate is a novel algorithm for reference-free quality assessment and filtering of de novo transcriptome assemblies.
TransRate downloads and documentation are available here
If you use TransRate in your work please cite:
Smith-Unna, R.D., Boursnell, C., Patro, R., Hibberd, J.M., and Kelly, S. (2015). TransRate: reference free quality assessment of de-novo transcriptome assemblies. In Review