Directed evolution offers a way to measure "fitness" of large numbers of synthetic sequences in parallel. Nanopore and other long-read sequencing technologies have the potential to probe distant epistatic interactions in such datasets, as well as resolving other genomic questions of interest in cancer, evolution, and other area of biology. I will describe our group's work in basecalling, analysis, and visualization of nanopore sequencing data, with an emphasis on synthetic biology applications.