I'm a director of a new bioinformatics core and I just wanted to start a general discussion here to hear others' thoughts.
What's the role of a bioinformatics core in a world of cloud computing and ultra-economy-of-scale genome factories (e.g. BGI, Complete Genomics)?
A recent article in GenomeWeb discusses Ion Torrent's (Life Technology) plans to enter the commercial bioinformatics arena, and their plans on launching a cloud-based variant analysis software package. (Article is paywalled, but free if you register with a .edu address).
Montana-based Golden Helix and Durham-based Expression analysis have teamed up to offer a service-based cloud computing solution for next-generation sequencing bioinformatics analysis. BusinessWire, GenomeWeb, GoldenHelix Webcast).
There are others competing in the commercial bioinformatics arena that I'm surely leaving off.
Genome factories bundling bioinformatics
I had meetings with reps from both BGI and Complete Genomics last week.
CG offers human whole-genome sequencing bundled with a very sophisticated bioinformatics pipeline that returns annotated variants, mapped reads with a local de novo assembly around variants, summary statistics, and summaries of evidence around called variants, indels, etc. Their price and value added by the bundled bioinformatics will be difficult to beat.
The BGI rep spoke of the cost reduction and throughput that they have with their massive economy of scale operation. Their sequencing services (DNA, RNA, epigenetics) all include bundled bioinformatics services.
What does a bioinformatics core need to do to thrive?
What does a core need to do to thrive when competing with other vendors that bundle bioinformatics costs with cheap sequencing? It may be too early to tell whether cloud computing services like Ion Reporter or GoldenHelix/ExpressionAnalysis will add any significant value to a sequencing service provider's offering, but these may also become a challenge in the near future for service-based cores.