diff --git a/.gitmodules b/.gitmodules
index 0f131ca11..1beea4569 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,9 +1,6 @@
 [submodule "fermi-lite"]
 	path = fermi-lite
-	url = https://github.com/walaj/fermi-lite
-[submodule "htslib"]
-	path = htslib
-	url = https://github.com/samtools/htslib
+	url = https://github.com/julianhess/fermi-lite.git
 [submodule "bwa"]
 	path = bwa
-	url = https://github.com/walaj/bwa
+	url = https://github.com/lh3/bwa.git
diff --git a/bwa b/bwa
index 609311b88..740d895fd 160000
--- a/bwa
+++ b/bwa
@@ -1 +1 @@
-Subproject commit 609311b8842244c5c15405b3ea553455f542f786
+Subproject commit 740d895fd98893bd05fe6cbf765b9d2e93f92323
diff --git a/fermi-lite b/fermi-lite
index 5bc90f8d7..ec0b8b327 160000
--- a/fermi-lite
+++ b/fermi-lite
@@ -1 +1 @@
-Subproject commit 5bc90f8d70e2b66184eccbd223a3be714c914365
+Subproject commit ec0b8b32787c05f97ca06157070dd49d9bdfa855