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Background  The sequencing,  de novo  assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate  de novo  assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of  de novo  transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species,  Nerita melanotragus,  and compared the assembly produced by four different  de novo  transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy.    Results  Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases  de novo  assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function.    Conclusions  We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate  de novo  transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers