diff --git a/pkgs/development/python-modules/HTSeq/default.nix b/pkgs/development/python-modules/HTSeq/default.nix
new file mode 100644
index 000000000000..7cbe523ba1ec
--- /dev/null
+++ b/pkgs/development/python-modules/HTSeq/default.nix
@@ -0,0 +1,20 @@
+{ stdenv, buildPythonPackage, fetchPypi, cython, numpy, pysam, matplotlib
+}:
+buildPythonPackage rec {
+  version = "0.11.2";
+  pname = "HTSeq";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc";
+  };
+
+  buildInputs = [ cython numpy pysam ];
+  propagatedBuildInputs = [ numpy pysam matplotlib ];
+
+  meta = with stdenv.lib; {
+    description = "A framework to work with high-throughput sequencing data";
+    maintainers = with maintainers; [ unode ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index efa8c4be0942..75f2afab0d7e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1698,6 +1698,8 @@ in {
     inherit (pkgs) pkgconfig;
   };
 
+  HTSeq = callPackage ../development/python-modules/HTSeq { };
+
   httpserver = callPackage ../development/python-modules/httpserver {};
 
   bleach = callPackage ../development/python-modules/bleach { };