diff --git a/src/main.cpp b/src/main.cpp
index b3d47e7..1718279 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -216,6 +216,7 @@ int main(int argc, char **argv) {
     size_t n_poa_threads = num_poa_threads ? args::get(num_poa_threads) : n_threads;
 
     std::string smoothed_out_gfa = args::get(smoothed_out);
+    std::filesystem::path smoothed_out_gfa_path = smoothed_out_gfa;
     std::vector<std::string> consensus_path_names;
     std::vector<smoothxg::consensus_spec_t> consensus_specs;
     bool requires_consensus = !args::get(vanish_consensus);
@@ -1024,13 +1025,13 @@ int main(int argc, char **argv) {
             std::string path_smoothed_gfa;
             if (current_iter < num_iterations - 1) {
                 consensus_path_names.clear(); // We need this only at the last iteration
-                const std::string patent_dir = args::get(tmp_base).empty() ?
+                const std::string parent_dir = args::get(tmp_base).empty() ?
                         filesystem::path(path_input_gfa).parent_path().string() :
                         args::get(tmp_base);
-                if (patent_dir == "") {
-                    path_smoothed_gfa = prefix + ".smooth." + std::to_string(current_iter) + ".gfa";
+                if (parent_dir == "") {
+                    path_smoothed_gfa = prefix + ".smooth." + std::to_string(current_iter) + ".og";
                 } else {
-                    path_smoothed_gfa = patent_dir + "/" + prefix + ".smooth." + std::to_string(current_iter) + ".gfa";
+                    path_smoothed_gfa = parent_dir + "/" + prefix + ".smooth." + std::to_string(current_iter) + ".og";
                 }
             } else {
                 path_smoothed_gfa = smoothed_out_gfa;
@@ -1038,7 +1039,13 @@ int main(int argc, char **argv) {
 
             std::cerr << smoothxg_iter << "::main] writing smoothed graph to " << path_smoothed_gfa << std::endl;
             ofstream out(path_smoothed_gfa.c_str());
-            smoothed->to_gfa(out);
+            // can write to gfa on the final iteration
+            if (current_iter == num_iterations - 1 && smoothed_out_gfa_path.extension() == ".gfa") {
+                smoothed->to_gfa(out);
+            }
+            else {
+                smoothed->serialize(out);
+            }
             out.close();
             delete smoothed;
 
diff --git a/src/prep.cpp b/src/prep.cpp
index 7992d8e..14bb918 100644
--- a/src/prep.cpp
+++ b/src/prep.cpp
@@ -1,4 +1,5 @@
 #include "prep.hpp"
+#include <filesystem>
 
 namespace smoothxg {
 
@@ -19,7 +20,17 @@ void prep(
 
     // load it into an odgi
     odgi::graph_t graph;
-    odgi::gfa_to_handle(gfa_in, &graph, true, num_threads, true);
+
+    std::filesystem::path graph_path = gfa_in;
+    std::cerr << smoothxg_iter << "::prep] Loading graph for prep " << gfa_in << std::endl;
+
+    if (graph_path.extension() == ".gfa") {
+        odgi::gfa_to_handle(gfa_in, &graph, true, num_threads, true);
+    } else {
+        ifstream f(gfa_in.c_str());
+        graph.deserialize(f);
+        f.close();
+    }
     graph.set_number_of_threads(num_threads);
 
     // sort it using a short sorting pipeline equivalent to `odgi sort -p Ygs`
@@ -144,10 +155,15 @@ void prep(
     odgi::algorithms::chop(graph, max_node_length, num_threads, true);
 
     std::cerr << smoothxg_iter << "::prep] writing graph " << gfa_out << std::endl;
+
+    graph_path = gfa_out;
     std::ofstream f(gfa_out);
-    graph.to_gfa(f);
+    if (graph_path.extension() == ".gfa") {
+        graph.to_gfa(f);
+    } else {
+        graph.serialize(f);
+    }
     f.close();
-
 }
 
 }