They currently specialize in different things. The larger Illumina instruments have a huge up-front cost (~$1M), tremendous throughput, low cost per base, short

They currently specialize in different things. The larger Illumina instruments have a huge up-front cost (~$1M), tremendous throughput, low cost per base, short reads, <1% base error, and significant latency between starting sample prep and getting results back. Nanopore sequencing has trivial up-front costs, same-day results, orders of magnitude higher cost per base, >10% non-independent error rate and very long reads. ONT will be much more useful for assembling reference genomes (which can then be polished with short reads), characterizing large scale structural variants, and real time applications like "what pathogen am I infected with?".