MinION Adventures Part 1
Contributed by Marina Becker
Recently, the Weimer Lab has acquired an Oxford Nanopore MinION to use as a sequencing resource for our research. So far, we are still in the preliminary stages of testing and using the device but we are making strides forward. We completed our lambda burn-in of the device this week and are excited to be continuing onto genomic sequencing.
There have been several hurdles that we have had to overcome in our journey so far. The first, and arguably most difficult, were computer hardware and software issues. We were initially unable to load the appropriate operating system onto the computer we purchased for the project. After many attempts to get Windows 7 properly installed, we decided to progress with Windows 8 (under beta support for the MinION) which has thus far not been problematic. Next, there was a bit of confusion regarding the protocol. It is worth noting that though they are HIGHLY SIMILAR, the protocols for lambda burn in and genomic DNA are different. We also encountered a common problem during lambda execution which is the creation of air bubbles during flow cell loading. A single bubble was observed during the loading and no amount of buffer shifting could resolve it. We opted to proceed with the run and have yet to determine how this affected the performance of the flow cell. Finally, we encountered a problem with the Metrichor weberver integration. As it turns out, only actively registered members of the MinION group can use Metrichor apps. This technical issue will be resolved pending the addition of all relevant members to the MinION owner’s group.
The overall process has been difficult but we have managed to get past all roadblocks we have encountered so far. The next hurdle will likely be in data analysis. We have several programs lined up for testing with the lamda burn-in reads including some new R packages for data type conversion and some old favorites for assembly and beyond.
For now, we press forward.
More information coming in MinION adventures Part 2!