Importing Cactus Alignments into vg

Modern versions of the Cactus aligner support the Minigraph-Cactus Pangenome Pipeline, so if you want to get a Cactus alignment into vg, you should use that pipeline's built-in ability to write vg-compatible .gbz files.

If you for some reason can't do that, you can use the hal2vg tool to import multiple sequence alignments from Cactus's Hierarchical Alignment (HAL) format.