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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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about reference-free questions #1358

Open HFzzzzzzz opened 2 months ago

HFzzzzzzz commented 2 months ago

Hello author, I have a question about reference-free methods. Progressive Cactus is a reference-free multi-genome alignment, and it seems to be independent of the reference genome during the alignment process. However, when converting from HAL to MAF, it needs to specify a reference genome. Does this mean that it actually depends on the reference genome to a certain extent? As for MiniGraph-Cactus, how does it depend on the reference genome? Is it also a reference-free pangenome process?

glennhickey commented 2 months ago

Progressive Cactus does not depend on a reference genome and the HAL file it outputs is reference free. Converting to MAF is reference dependent (you can choose any genome as reference) because MAF is, in practice, a reference-based format.

Minigraph-Cactus uses a reference genome to structure the graph and is therefore not reference free. The minigraph-paper goes into this subject in detail (you can find links in the README and a preprint on biorxiv).