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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg giraffe mapping HiFi #4227

Closed brettChapman closed 4 months ago

brettChapman commented 4 months ago

Hi

I have some HiFi sequences, and was wondering if it's possible to align long reads to a genome graph, such as those produced from minigraph-cactus, or is it only designed for short read sequences? If not, are there plans to accommodate long reads?

Thanks.

jeizenga commented 4 months ago

The current default vg giraffe is really tailored specifically to short reads. It will run on long reads, but it will not be efficient. We are actively working on new algorithms for accurate long reads like HiFi, but the new features are still experimental. We aren't yet maintaining a consistent interface, and the performance may fluctuate unpredictably as we continue development.