At the DNA Technologies Laboratory at the National Research Council of Canada, scientists are using the Pippin size selection platform to improve the quality of their genome assemblies.
Andrew Sharpe, Research Officer and Group Leader
of the Saskatoon-based laboratory, got his first Pippin Prep last year. He added a second Pippin Prep as well as the longer-fragment Blue Pippin to his arsenal earlier this year.
In Sharpe’s lab, which also serves as a core facility for NRC and other Canadian government agencies, assembly projects tend to focus on large plant and fungal genomes. His team relies on Illumina and 454 sequencing, often adopting a hybrid assembly approach to take advantage of both platforms.
“The majority of libraries going through are the shorter, standard pair-end libraries of 200 to 400 bases,” Sharpe says, noting that those libraries run on all three Pippin machines. Longer mate libraries — usually in the range of 3kb to 10 kb — are also a good fit for the Pippin, he adds.
Sharpe and his colleagues use the Pippin platform to create multiple pair-end libraries for the same sample — constructing, for instance, three libraries with 200-base, 300-base, and 400-base inserts — and then assemble all of those sequences together, often using SOAPdenovo. “If you assemble one of the libraries, then you’ll end up with an assembly. But if you assemble all three together using three different lengths, you get quite a bit better product,” Sharpe says. “The nice thing with the Pippin Prep is being able to easily get those discrete size ranges.”
Before Sharpe had the Pippin, his team spent a lot of time on manual gel extractions. “Having the Pippin makes things quite a lot more efficient on the labor side,” he says. Now he’s looking to the Blue Pippin to take over for the field inversion gel electrophoresis his team runs for making larger 454 mate libraries. “The Blue Pippin offers the prospect of actually speeding up that process and hopefully getting away with less amounts of DNA,” Sharpe says. “You normally need a lot of DNA to operate on the standard FIGE gel, but with the Blue Pippin we should be able to get away with less.”