The software tool described in this new arxiv paper is exactly what we need today for our work. It allows one to remove clutter from de novo RNAseq assemblies.
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input, TransRate measures the quality of individual contigs and whole assemblies, enabling assembly optimization and comparison. TransRate can accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species. We show that it is more accurate than comparable methods and demonstrate its use on a variety of data.