From 758b133301ac5eb36fd1f9b1a2da67e97ecb32a0 Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Thu, 30 Mar 2023 14:51:25 +0200
Subject: [PATCH] Update file phylo_exercise.md

---
 exercises/phylo_exercise.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/exercises/phylo_exercise.md b/exercises/phylo_exercise.md
index ea19b2a..c1bb4c9 100644
--- a/exercises/phylo_exercise.md
+++ b/exercises/phylo_exercise.md
@@ -203,6 +203,21 @@ Change the variables to your needs.
 
 
 
+### DOWNLOAD TREE FILES
+
+The complete output for the SNP calling, MSA and tree can be found here, download it into a `[target_directory]` of your choice. 
+
+```bash
+# Typestrain as reference
+cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/03_output_mrsa/snippy_ref_typestrain [target_directory]
+
+# Hybrid assembly as reference
+cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/03_output_mrsa/snippy_ref_hybrid [target_directory]
+```
+
+
+
+
 
 
 
-- 
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