diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
new file mode 100644
index 000000000000..05a85cafedf1
--- /dev/null
+++ b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, zlib, tbb }:
+
+stdenv.mkDerivation rec {
+  pname = "bowtie2";
+  version = "2.3.3.1";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "BenLangmead";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1pcyks76bnnkq6h0gqjw4fkdddjjnw7k5ibim7ajkbvfw58a99y0";
+  };
+
+  buildInputs = [ zlib tbb ];
+
+  installFlags = [ "prefix=$(out)" ];
+
+  meta = with stdenv.lib; {
+    description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
+    license = licenses.gpl3;
+    homepage = http://bowtie-bio.sf.net/bowtie2;
+    maintainers = with maintainers; [ rybern ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1ff3da0c13e2..2a961dd1ce00 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -762,6 +762,8 @@ with pkgs;
 
   bootchart = callPackage ../tools/system/bootchart { };
 
+  bowtie2 = callPackage ../applications/science/biology/bowtie2 { };
+
   boxfs = callPackage ../tools/filesystems/boxfs { };
 
   brasero-original = lowPrio (callPackage ../tools/cd-dvd/brasero { });