diff --git a/ipyrad/core/params.py b/ipyrad/core/params.py
index 33c3b174..92c5d53c 100644
--- a/ipyrad/core/params.py
+++ b/ipyrad/core/params.py
@@ -42,7 +42,7 @@ def __init__(self):
             ("demultiplex_on_i7_tags", False),
             ("declone_PCR_duplicates", False),
             ("merge_technical_replicates", True),
-            ("exclude_reference", False),
+            ("exclude_reference", True),
             ("trim_loci_min_sites", 4),
         ])