diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp
index db9d7c68a..f1787c5be 100644
--- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp
+++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp
@@ -181,6 +181,8 @@ DBGSSHash::DBGSSHash(const std::string &input_filename,
         auto is_breakpoint = [this,canonical=std::move(canonical)](node_index node) {
             if (canonical) {
                 return !canonical->has_single_incoming(node) || !canonical->has_single_incoming(reverse_complement(node));
+            } else if (mode_ == CANONICAL) {
+                return !has_single_incoming(node) || !has_single_incoming(reverse_complement(node));
             } else {
                 return !has_single_incoming(node);
             }