diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index f9615a8e0e..0000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,9 +0,0 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
-[submodule "sdsl-lite"]
-	path = submodules/sdsl-lite
-	url = https://github.com/xxsds/sdsl-lite
-[submodule "cereal"]
-	path = submodules/cereal
-	url = https://github.com/USCiLab/cereal
diff --git a/submodules/cereal b/submodules/cereal
deleted file mode 160000
index ebef1e9298..0000000000
--- a/submodules/cereal
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ebef1e929807629befafbb2918ea1a08c7194554
diff --git a/submodules/sdsl-lite b/submodules/sdsl-lite
deleted file mode 160000
index 7e07a14579..0000000000
--- a/submodules/sdsl-lite
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7e07a14579c31cefad0ec6fa2b2e3e78dbbc1a68