Imagine that I work on an organism without a reference genome, and that the closest reference genome I can get is quite diverged. E.g. ~10% diverged in terms of SNVs when measured with short reads, and also has a lot of structural variants too.
Now imagine I get a 1 million base-pair long-read (e.g. from Nanopore data) for my organism. The question is this:
How can I estimate the proportion of the read that is meaningful sequence vs garbage?
Some things that probably won't work
Most standard approaches won't work here. E.g. I could try mapping the read to the reference, but even if the read was perfectly good I wouldn't expect most of it to map thanks to true structural variations between the read and the reference. The same goes for standard alignment or BLAST.
Some things that might work
The best naive method here seems to be to cut the read up into smaller pieces (either overlapping or not) and use standard approaches to map/align each of these.
So, what have people tried for this? And what tools have you used and why?