diff --git a/pkgs/applications/science/biology/bowtie/default.nix b/pkgs/applications/science/biology/bowtie/default.nix
new file mode 100644
index 00000000000..964eeddb461
--- /dev/null
+++ b/pkgs/applications/science/biology/bowtie/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, fetchFromGitHub, zlib }:
+
+stdenv.mkDerivation rec {
+  pname = "bowtie";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "BenLangmead";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0da2kzyfsn6xv8mlqsv2vv7k8g0c9d2vgqzq8yqk888yljdzcrjp";
+  };
+
+  buildInputs = [ zlib ];
+
+  installFlags = [ "prefix=$(out)" ];
+
+  meta = with stdenv.lib; {
+    description = "An ultrafast memory-efficient short read aligner";
+    license = licenses.artistic2;
+    homepage = "http://bowtie-bio.sf.net/bowtie";
+    maintainers = with maintainers; [ prusnak ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 06c84a16221..c1f63d2df10 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1616,6 +1616,8 @@ in
 
   boot = callPackage ../development/tools/build-managers/boot { };
 
+  bowtie = callPackage ../applications/science/biology/bowtie { };
+
   bowtie2 = callPackage ../applications/science/biology/bowtie2 { };
 
   boxfs = callPackage ../tools/filesystems/boxfs { };