Sequencing your DNA with a USB dongle and open source code #DNA #OpenSource @stackoverflow

Remember the scene from the Matrix where Neo unlocks his full power, and the world around him is revealed as lines of code running in all directions? What if you could see the world around you in this way?

Recent breakthroughs in nanopore sequencing, driven by developments in open-source software, have made it possible to greatly reduce the time it takes to decode a genome, shrinking what used to be a 15-day process to three days or less. It wasn’t so long ago that decoding a genome took years! To understand the code behind these new techniques, which have been dubbed UNCALLED, we chatted with Prof. Michael Schatz, the Bloomberg Distinguished Associate Professor of Computer Science and Biology at Johns Hopkins.

Imagine a hole so tiny that a single strand of DNA can fit through at a time. Push your genetic material through this pore, and the As, Ts, Gs, and Cs that make up a human genome will be revealed in sequence. So, how do you tell the four building blocks of DNA apart?

“It takes the most exquisite measurements you can imagine, measuring the changes in current associated with different bits of DNA,” he explains. “This is happening at the level of pico-amps—one-trillionth of an amp measurement—and we can get these readings in real time.” Five years ago, the equipment needed for this work would have been restricted to serious research facilities. Today, for about a thousand dollars, you can purchase a nanopore sequencer as a peripheral that connects to any computer via USB.

The current climate is far healthier and happier for academics like Schatz, who plans to continue open sourcing the software being created by his lab. “There’s just so much benefit from being able to share code and work collaboratively.

Read more on the StackOverflow Blog


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