From 97dd47315a558a7a66c9f8a45c1b993112f212f0 Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Thu, 30 Mar 2023 10:30:22 +0200
Subject: [PATCH] Update file phylo_exercise.md
---
exercises/phylo_exercise.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/exercises/phylo_exercise.md b/exercises/phylo_exercise.md
index f269edb..844011e 100644
--- a/exercises/phylo_exercise.md
+++ b/exercises/phylo_exercise.md
@@ -68,7 +68,7 @@
```
# GENERATE A CORE SNP ALIGNMENT
- snippy-core --prefix core [outdir] [outdir2] [outdir3]
+ snippy-core --prefix core [outdir] [outdir2] [outdir3] --ref [reference]
```
This command will give you various output, but among them is `core.aln` and `core.full.aln`. Both are fasta multiple sequence alignment, the first contains only the core SNPs, the other contains the full alignment of your reference and the samples inlcuding any invariant sites.
--
GitLab