Our lab got a trial of the CLCbio Genomics software and we are using it to do de novo assembly in sugarcane RNA-seq data as well as analyzing the differentially expressed genes between two genotypes, contrasting to the response to drought. The software is very user friendly and easy to use, but I'd like to know if is as reliable as the other softwares commonly used for these analyses. Thanks since now.
I've tried CLC package and I agree it's straightforward to use. Graphical interface is helping a lot in case of inexperienced user. However, if you have bioinformatician in your lab I would recommend using free software ie. Velvet for de novo assembly and cufflinks pipeline for differential expression analyses. First of all, both packages are highly configurable, regularly updated and often offer more features than commercial tools. Secondly, these tools has been published, well documented and widely tested. Finally, most of the research in the field are done this way nowadays, but of course you will need trained technician/researcher.
For my data (~20Mb fungal genomes) I found Velvet performing much better than CLC. Moreover data managment sometimes is a pain with CLC. Of course, another assemblers might perform better depending on various scenarios.
We have used CLC as one of the tools for de novo assembly. With our data, it performed OK with Illumina data (and better than any other de Bruijn assembler we tried), but didn't do as well as Newbler for 454 data. We're still not entirely done yet, though.
Edit: this is from de novo genome assembly --- I missed that your question was concerning transcriptome sequencing.