There have been a couple of older posts similar to this topic, although they are older (over 2 years) and lacking in any real comparisons. I am hoping that given how much NGS sequencing has matured in the last few years, in particular clinical applications, some people may have some more concrete experience and info to provide. I am currently part of a working group for a regional hospital that is looking to implement NGS-based testing in their molecular diagnostics laboratory. Will be starting with a bench-top sequencer (either MiSeq or Ion Torrent most likely) and will be dual use (research/clinical). Most clinical applications will likely be in oncology at least initially. As the local bioinformatics expert for human NGS applications I am evaluating what will fit their needs best. I believe there is support for bioinformatics staffing as part of the setup. As a bioinformatician I am leary of unpublished algorithms and black boxes. While commercial packages like CLC Workbench and Nextgene are very easy to use I don't like not knowing what is going on with my data.
Does anyone have any direct experience comparing the results of packages like Nextgene for instance with pipelines using published open-source software? I think open source solutions like bcbio-nextgene are particularly suited for this type of thing. Especially if thinking with long-term scalability and growth in mind.