Gabe Rudy’s webcast yesterday, Big Data at Golden Helix: Scaling to Meet the Demand of Clinical and Research Genomics, was a huge success with well over 300 registered. In today’s blog post, I wanted to recap the Q&A session with Gabe. If you missed the webcast, check it out!
Question: What is the end goal for an application like Warehouse?
Answer: The end goal is to essentially scale with the needs of labs. For a large lab, this may be to integrate with an existing system like a LIMS or EMRS. It is also scaling to meet the needs of smaller labs and different types of groups such as research institutions versus more clinical settings.
Question: When do you see the move from clinical whole exome to clinical whole genome unfolding?
Answer: While it is a matter of cost, it is also a matter of the level of comfort with being able to handle the massive increase in data size. Instead of looking at tens of thousands or a hundred thousand variants in a whole exome, you are looking at tens of millions of variants in a whole genome. In terms of price curve, it has flatlined a bit due to the state of competition in the marketplace. However, as technology increases and improvements in chemistry are made in things such as reagents costs, it is only a matter of time before the price falls.
Question: Impressive technology, but I run a small lab. Do you have versions of your software that will fit into an affordable budget?
Answer: Yes, we are working with labs that range greatly in size. Some labs may have only a few members who need analysis access. Other labs have many members that need hands-on access to tools. Stay tuned as we are putting new packages together to meet the needs of all labs.
Question: Are these features in your software now? If not, when are they going to be available?
Answer: All of the features presented are available now! Please let us know if you are interested in evaluatiing one of our tools.
Question: Approximately how many VCF files can VarSeq analyze simultaneously?
Answer: Raw VCF files only need to be handled during initial import. We have worked hard to scale that to not be an upper bound. So essentially, unbounded. We are very happy that some of our customers are pushing the limits.
Question: Are VarSeq and the VSWarehouse ready for livestock?
Answer: We have annotations that span many species (bovine, ovine, gallus, etc) and all of our tools are aware of which reference assembly the variants are aligned to and only the appropriate annotations are brought in. While there are a lot of clinical workflows that do not make sense in regards to livestock, VarSeq and Warehouse can handle your samples regardless of where they are coming from.
If you are interested in giving one of our software solutions a try, please email us at firstname.lastname@example.org.