Very simple set-up: We have PacBio long high-fidelity (HiFi) reads, genome sequencing, and some of those that contain a particular sequence. I want to find out which ones. The length of the query sequence is 7kb, though ideally I would use as query a sub-sequence of only 1.5kb.

The output can the just the read ID or the full read sequence.

We tried [DAMAPPER][1] and it gives some decent results but it might not be appropriate to search for the shorter sub-sequence of 1.5kb. It also feels like an overkill for this purpose. 

Bare in mind that this is my first foray in long-read sequencing so my mindset is still very much one of short low error-rate reads.

  [1]: https://github.com/thegenemyers/DAMAPPER