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first, SyRI is a pairwise structural variant caller. For looking at multiple samples, plotsr can be useful, but syri itself does not currently consider more than two genomes.
Re comparing different species, in principle, there's nothing stopping you, so long as they have a (mostly) shared chromosomal architecture and you can get a decent alignment of the genomes using eg minimap2 or mummer.
SyRI is however first and foremost a synteny detection tool, thus the output may be hard to interpret or nonsense if you compare two genomes that do not have any synteny.
Ultimately, it depends on what the objective of your comparison is and which kind of species you are thinking about comparing – Arabidopsis vs maize is quite a different problem from human vs chimp.
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lrauschning commentedon Nov 12, 2025
Hi @zuodabin,
first, SyRI is a pairwise structural variant caller. For looking at multiple samples, plotsr can be useful, but syri itself does not currently consider more than two genomes.
Re comparing different species, in principle, there's nothing stopping you, so long as they have a (mostly) shared chromosomal architecture and you can get a decent alignment of the genomes using eg minimap2 or mummer.
SyRI is however first and foremost a synteny detection tool, thus the output may be hard to interpret or nonsense if you compare two genomes that do not have any synteny.
Ultimately, it depends on what the objective of your comparison is and which kind of species you are thinking about comparing – Arabidopsis vs maize is quite a different problem from human vs chimp.
Cheers,
Leon