diff --git a/pkgs/applications/science/biology/stacks/default.nix b/pkgs/applications/science/biology/stacks/default.nix
new file mode 100644
index 000000000000..01b1c0ba81bf
--- /dev/null
+++ b/pkgs/applications/science/biology/stacks/default.nix
@@ -0,0 +1,19 @@
+{ stdenv, fetchurl, zlib }:
+    
+stdenv.mkDerivation rec {
+  pname = "stacks";
+  version = "2.3e";
+  src = fetchurl {
+    url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
+    sha256 = "046gmq8nzqy5v70ydqrhib2aiyrlja3cljvd37w4qbd4ryj3jr0w";
+  };
+
+  buildInputs = [ zlib ];
+
+  meta = {
+    description = "Software pipeline for building loci from short-read sequences";
+    homepage = http://catchenlab.life.illinois.edu/stacks/;
+    maintainers = [ stdenv.lib.maintainers.bzizou ];
+    license = stdenv.lib.licenses.gpl3;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 33464ab30a45..0e3c147593c8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21717,6 +21717,8 @@ in
 
   somatic-sniper = callPackage ../applications/science/biology/somatic-sniper { };
 
+  stacks = callPackage ../applications/science/biology/stacks { };
+
   star = callPackage ../applications/science/biology/star { };
 
   strelka = callPackage ../applications/science/biology/strelka { };