diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index aac36d2af310..92cb420139df 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
-  version = "2.30.0";
+  version = "2.31.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "sha256-NqKldF7ePJn3pT+AkESIQghBKSFFOEBBsTaKEbU+oaQ=";
+    sha256 = "sha256-LBD3z0+zGbQJ67oyPRFPgbiMY9EP17vSk1EKz3DrkEc=";
   };
 
   strictDeps = true;