does vg giraffe support the third mapping of precise long reads (PacBio HiFi, ONT) to graph-based pan-genomes?

[ChenDepp]

@jeizenga
hello, I read about issues with mapping long reads for pan-genomes, so I was wondering if the new version of vg giraffe supports mapping long reads.
https://github.com/vgteam/vg/issues/4054
waiting for your reply! thanks

[jeizenga]

There are experimental features for long read mapping in vg, but nothing mature yet. It's an active area of development, and I expect there will be a well-functioning version of vg giraffe for long reads relatively soon. Until then, I would recommend GraphAligner for long read mapping to pangenome graphs. There's also a recently developed tool called PanAligner, whose performance I'm not familiar with yet.