diff --git a/pkgs/applications/science/biology/xenomapper/default.nix b/pkgs/applications/science/biology/xenomapper/default.nix
new file mode 100644
index 000000000000..cc235c4ca996
--- /dev/null
+++ b/pkgs/applications/science/biology/xenomapper/default.nix
@@ -0,0 +1,23 @@
+{buildPythonPackage, lib, fetchFromGitHub, statistics}:
+
+buildPythonPackage rec {
+  pname = "xenomapper";
+  version = "1.0.2";
+
+  src = fetchFromGitHub {
+    owner = "genomematt";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0mnmfzlq5mhih6z8dq5bkx95vb8whjycz9mdlqwbmlqjb3gb3zhr";
+  };
+
+  propagatedBuildInputs = [ statistics ];
+
+  meta = with lib; {
+    homepage = "http://github.com/genomematt/xenomapper";
+    description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins";
+    license = licenses.gpl3;
+    platforms = platforms.all;
+    maintainers = [ maintainers.jbedo ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index e0a8499e2a04..706e63787a11 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -6173,6 +6173,8 @@ in {
 
   yattag = callPackage ../development/python-modules/yattag { };
 
+  xenomapper = disabledIf (!isPy3k) (callPackage ../applications/science/biology/xenomapper { });
+
   z3 = (toPythonModule (pkgs.z3.override {
     inherit python;
   })).python;