Are there any de novo genome assemblers that work with both Nanopore and Illumina reads?
SPAdes can take both Nanopore and Illumina reads, but it's only for prokaryotic genomes. I haven't seen anything for eukaryotic.
All the discussion and literature that I have seen so far suggests using Nanopore long reads for assembly and then polishing with Illumina short reads. However, you need a certain level of coverage for the assembly to complete (for example, Canu recommended minimum is 20X). What if you only have 1X coverage with long reads? That will not be enough to assemble on its own, but should be much better than short reads alone. What's the appropriate approach for that situation?