In my group (synthetic biology), we are using Nanopore MinION to do (a) Hybrid assembly and (b) Sequencing of bar codes/transcription units in iterative synthet

In my group (synthetic biology), we are using Nanopore MinION to do (a) Hybrid assembly and (b) Sequencing of bar codes/transcription units in iterative synthetic biology design. For use case of hybrid assembly, we find that when you need not only an accurate but also contiguous denovo assembly. Hybrid assembly works really great because you're combining the best of both worlds, accurate short illumina sequencing and to span the gaps or ambiguous paths across contigs; use the Nanopore longer reads. This is important for use cases such as genomic surveillance of novel changes (e.g., synthetic engineering or horizontal or foreign gene transfer) - as you can't rely on a reference genome but need to detect a small change in the genome in an denovo fashion. For use case of iterative synthetic biology design, we find that Illumina short reads don't cut it when you're doing a high throughput screen sequencing of a pool of say synthetic genes where they have similar barcodes, promoters or gene sequences (you're screening for which family of enzyme would work best, so you end up with sometime very homologous sequences). Because Illumina's 100-250bp doesn't span the entirety of a sequence and having a pool of very similar sequence makes the demultiplexing very tricky. We used Nanopore and the results were mixed given the high error rate of MinION. Just sharing b/c it's been interesting to hear other people's application of Nanopore MinION!