From 803ffbd9d759631ac140f69f41a8ea1b6fa5e253 Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Mon, 2 Sep 2024 08:28:14 -0500 Subject: [PATCH] mention pansn --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 85d5f391..6f0458ca 100644 --- a/README.md +++ b/README.md @@ -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