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mention pansn
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ekg committed Sep 2, 2024
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Expand Up @@ -54,6 +54,7 @@ Specifying `-m, --approx-map` lets us stop before alignment and obtain the appro

Together, these settings allow us to precisely define an alignment space to consider.
During all-to-all mapping, `-X` can additionally help us by removing self mappings from the reported set, and `-Y` extends this capability to prevent mapping between sequences with the same name prefix.
When working with large sequence collections we frequently use [PanSN](https://github.com/pangenome/PanSN-spec) naming convention and `-Y'#'` to specify that we want to group mappings by prefix, which in this context means genome or haplotype groupings.


## input indexing
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