With the rise of NGS technologies, the transcriptomes of non-model organisms can be reconstructed even with the absence of a reference genome, using de novo assembly tools. There is a wide range of de novo assembly tools frequently being developed, however, there is a still a knowledge gap about the different effects and efficiency of different de novo assembly software types for RNA-seq assembly. This study aims to assemble the transcriptome of two different mussel species, Anodonta anatina and Margaritifera margaritifera, using three different types of genomic assemblers and to evaluate their distinct performances. Here, the transcriptomes have been assembled using whole-genome, single-cell and RNA-seq specific assemblers, and the results have been evaluated and compared using reference-free transcriptome evaluation tools. Whole-genome assemblers are not designed to handle variable transcript expressions and splice variations, and have thus achieved poor performance at assembling the transcriptomes. Single-cell assemblers, however, are designed to assemble genomes with uneven coverage, which make them able to handle variable transcript expressions and have therefore achieved good efficiency at assembling the transcriptomes. Single-cell assembler SPAdes has matched the performance of the well stablished RNA-seq assembler Trinity and the single-cell version of IBDA performed just as well as their RNA version. Overall, the top performing assembler in the study was the RNA version of SPAdes.