9.6 years ago by
I am presently going the opposite way from what you do, coming from CLC, I am exploring (anew) the possibilities of open software (mainly mira3 now) for 454 assembly.
I work in a lab mainly into evolution and genomics in fishes. We have been using CLC Genomic Workbench for the last year with great results. The software IS really a well integrated resources with a lot of small functionalities. Nothing that you couldn't find in the open source world, but well put together.
We have mostly used the software to toy with RNA-seq 454 data in non-model species, so our expertise is with de-novo assembly of expressed sequences, namely cDNA from RNA containing poly-A tails.
I would say that the main strength of CLC is it's easiness of use, mainly for non-computer-oriented biologists, or even for non-hardcore-linux users. For example, using menus, it is easy to import .sff or fasta/fasta.qual data, trim sequences according to different criteria, do a de novo assembly, save consensus sequences from the contigs, do a reference assembly (possibly with only a subset of sequences), look for SNPs, export SNP tables and ACE assembly files. This we have done repeatedly and new comers in the lab get quickly to their results without too much of a chock. It is, however, highly suggested to use the software on a 64 bit system with plenty of ram (8 gigs and up).
All this comes at the price of some flexibility and some transparency, I guess. The reason I am looking into mira3 now is that, it appears that the de novo alignment algorithm is not totally appropriate for RNA-seq projects. The steps involved in the alignment lead to more gene chimeras and strange coverage patterns within each contig that may be expected from a 'correct' approach.
Overall, our experience with CLC HAS been very satisfactory and we will likely continue to use it in the near future. As you mention, the scary (at first) cost of the license compares lightly to the total cost of one (not mentioning that you will probably use it for many) next gen projects.
Hoping this helps :)
(don't hesitate to share your ideas on mira3 or other open software also :)