In this blog series, we’ve been looking at how Sage Science customers use their Pippin Prep and BluePippin instruments with their Illumina sequencers. Today we check out the Nextera workflow, which is designed for speedy NGS sample prep. It can yield even better results with a Pippin size selection step.
We visited Zach Herbert, associate director of the genomics core facility at Dana-Farber Cancer Institute, to learn more about how he built a Nextera+Pippin pipeline. He deploys the Nextera tagmentation protocol for small genomes and larger amplicon projects that come to the core lab. Herbert found that adding a size selection step with Pippin Prep afterward led to very tightly sized libraries. This method is a boon for reproducibility, MiSeq flow cell clustering, and data analysis.
Herbert also uses Pippin when he’s running samples together. Attempting to pool samples with a broad size range in equimolar amounts is very tricky — “but if all those libraries are the same size, then we’re much more likely to get an even distribution of that pool,” he told us.
Pippin and Nextera also work well together for mate-pair sequencing. Illumina recommends using the Pippin platform to get “more stringent” sizing than can be accomplished with AMPure alone. (You can find us under Size Selection in Chapter 3, beginning on page 40 of the guide.)
Check back soon for our next blog in this series. We’ll be looking at using Pippin in the Illumina sequencing pipeline for double-digest RAD-seq, ChIP-seq, and more.