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Very simple set-up: We have a 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 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.

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

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I have seen the blasr aligner typically used for aligning PacBio reads to a reference. Is there a reason why blasr would not be a good choice? I guess the very short sequence you are trying to align to might be an issue.

Minimap2 is capable of mapping pacbio reads, and can also do pairwise mapping to see if reads overlap with each other, so this function might help you: From https://github.com/lh3/minimap2

minimap2 -x ava-pb  reads.fq query_seq.fq > ovlp.paf
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