If Sequencing technologies were food…

Over the years, I’ve become more of a foodie than I used to be. I always had an interest in food, but it wasn’t until I started cooking for my wife after we met back in 2002 that I started investing the time and energy into it.

In any case, I got to thinking about what kind of food best describes each Next-gen sequencing technology. Yes, it’s silly, but hey – it’s fun! Here goes.

In no particular order:

  • Complete Genomics – Meatloaf: Complete Genomics is a love hate relationship for me. They’re the company that most understands social media, that has the most realistic vision of their technology, and a simple plan for moving forward. Like meatloaf, they may well be the food for the masses. However, they’re also the one company that has the least exciting technology. Yes, they are doing neat things with their tech – but the technology isn’t going to surprise anyone who studied biochemistry in the 1990’s. They really are the boring meatloaf of the sequencing world – but wow, who knew you could do that with meatloaf?
  • Illumina – sushi: If you don’t live on the west coast, you might not get this. Here, in Vancouver, sushi is a staple. There’s a sushi restaurant on every corner, competing with Starbucks for real estate. When I think of Illumina, sushi just makes sense as a good comparison: the machines are plentiful, and the quality can vary according to where you go. The early illumina sequencing data sets kinda left an off-taste in your mouth, but the quality has increased while the price has dropped, just like sushi. Also like sushi, Illumina is clearly the mainstay, and about as plentiful as the sushi shops in Vancouver. mmm…sushi.
  • 454/pyrosequencing – Greasy diner food: You know, diner food is hit or miss. My first next-gen experiences were with 454, and in hindsight, were a complete waste of time. That’s not to say it’s all garbage, but like Illumina, it had to mature. If you’ve ever watched the food network, you’ll probably have come across the show “Diners, Drive-ins and Dives”, you’ll know that you can get some pretty high-end greasy diner food. For me, 454 has gone from the worst of the dives to being a pretty decent greasy-spoon. I wouldn’t want to eat it every meal, but I’m happy to do it once in a while, as long as we balance it with some veggies, or maybe some sushi. (-:
  • SOLiD – Chinese food: Most people think of stuff like Lemon-Chicken, or spring rolls as typical chinese food, but SOLiD reminds me of Chinese wedding food. It’s finicky and doesn’t always work – and isn’t accessible for everyone. eg. Chicken Feet just isn’t my thing. Of course, if you’re a chinese banquet chef, you can get it working and you get some pretty fantastic food, but it seems that it takes a lof of finicky work to get it looking and tasting good. Those who like it like it, like it a lot. Much like Chinese food, you either get it or you don’t. My limited experience with SOLiD data tells me that it’s a pain in the back end to work with, but pretty rewarding when it finally all comes together.
  • Pacific Biosciences – SoufflĂ©.: I still think of PacBio as my favourite of the technologies. It’s the one that I most want to see succeed, and that has the most “neat” technology. Kind of having Star Trek technology materialise in front of your eyes. Unfortunately, it’s also the one that appears to have the most roadblocks in the sense that it seems hardest to get good meaning out of. As a food, for me, it would be a soufflĂ©. Personally, I’m not sure how much effort would be required to get it to work, nor if the end result will be the perfect meal or if it’ll all collapse flat and fail miserably. That said, I know it has the potential to be the best damn meal ever, if only the risk/uncertainty can be surmounted.
  • Oxford Nanopore – Astronaut ice-cream: Nanopore is the food that everyone tells me is great, that is completely space-age, completely revolutionary – and yet I just don’t see it at the grocery store. The concept is neat, but I just don’t know who’s buying it yet. Is it even available? Obviously I’m shopping at the wrong place.
  • Ion Torrent – A baguette… after MacGyver has jury rigged it to be the wings of a supersonic air plane. That is to say, they’ve made something fantastic out of what appear to be very basic ingredients. Seriously, they do some neat stuff with computer chips and it is pretty damn cool. They’ve used what appears to be off the shelf parts and some seriously fantastic engineering to deliver a really awesome platform. What can I say, I’m looking forward to sandwiches sponsored by Ion Torrent at a conference one day – it’ll be some fine food, I’m sure.
  • Sanger/ABI – McDonalds basic burger: I probably didn’t need to include this one, but it’s pretty clear where it’s at. Using Sanger sequencing today is pretty un-fulfilling. It’s cheap, it’s quick, and it just takes care of a very minimal need. Much like the assembly line burger at McDonalds – it’ll fill you up and take care of a burning hunger… but it’s not gourmet, and leaves you less than filled – but it’s cheap. I’m not convinced it’s more reliable than any the next gen – but it’s familiar and consistent.

All in all, it’s a pretty strange menu. Did I miss anything? Feel free to add your own food analogies.

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