diff --git a/lib/chopper b/lib/chopper
index ef728145..ac23ff7e 160000
--- a/lib/chopper
+++ b/lib/chopper
@@ -1 +1 @@
-Subproject commit ef728145557372a4e7f82def1d3a3743ae0198eb
+Subproject commit ac23ff7e9afb326bbc120dbb372c4720e544c6da
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index cf2498d3..494aeb4d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -32,6 +32,10 @@ set (CHOPPER_BUILD_TEST
      OFF
      CACHE BOOL "Build chopper tests."
 )
+set (CHOPPER_INSTALL
+     OFF
+     CACHE BOOL "Install Chopper."
+)
 
 FetchContent_MakeAvailable (raptor_chopper_project)
 
@@ -42,7 +46,7 @@ FetchContent_Declare (raptor_xxhash_project SOURCE_DIR "${RAPTOR_SUBMODULES_DIR}
 
 set (XXHASH_BUILD_ENABLE_INLINE_API ON)
 set (XXHASH_BUILD_XXHSUM OFF)
-set (XXHASH_BUNDLED_MODE OFF)
+set (XXHASH_BUNDLED_MODE ON)
 set (BUILD_SHARED_LIBS OFF)
 
 FetchContent_MakeAvailable (raptor_xxhash_project)
diff --git a/src/layout/raptor_layout.cpp b/src/layout/raptor_layout.cpp
index 53a85990..d864a601 100644
--- a/src/layout/raptor_layout.cpp
+++ b/src/layout/raptor_layout.cpp
@@ -35,12 +35,21 @@ void chopper_layout(sharg::parser & parser)
     config.disable_sketch_output = !parser.is_option_set("output-sketches-to");
 
     chopper::layout::layout hibf_layout{};
+    std::vector<std::string> filenames{};
+    std::vector<size_t> kmer_counts{};
+    std::vector<chopper::sketch::hyperloglog> sketches{};
 
-    chopper::data_store store{.false_positive_rate = config.false_positive_rate, .hibf_layout = &hibf_layout};
+    chopper::sketch::read_data_file(config, filenames);
 
-    chopper::sketch::execute(config, store);
-    chopper::sketch::estimate_kmer_counts(store.sketches, store.kmer_counts);
-    chopper::layout::execute(config, store);
+    chopper::sketch::execute(config, filenames, sketches);
+    chopper::sketch::estimate_kmer_counts(sketches, kmer_counts);
+
+    chopper::data_store store{.false_positive_rate = config.false_positive_rate,
+                              .hibf_layout = &hibf_layout,
+                              .kmer_counts = kmer_counts,
+                              .sketches = sketches};
+
+    chopper::layout::execute(config, filenames, store);
 }
 
 } // namespace raptor
diff --git a/test/unit/cli/build/build_hibf_chopper_test.cpp b/test/unit/cli/build/build_hibf_chopper_test.cpp
index 35aabeb0..1ad66e96 100644
--- a/test/unit/cli/build/build_hibf_chopper_test.cpp
+++ b/test/unit/cli/build/build_hibf_chopper_test.cpp
@@ -32,7 +32,6 @@ TEST_F(build_hibf_layout, pipeline)
         cli_test_result const result = execute_app("raptor",
                                                    "layout",
                                                    "--kmer-size 19",
-                                                   "--column-index 2",
                                                    "--threads 1",
                                                    "--input-file",
                                                    data_filename,