diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
new file mode 100644
index 00000000000..cd5c980b001
--- /dev/null
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -0,0 +1,25 @@
+{stdenv, fetchFromGitHub, zlib, python}:
+
+stdenv.mkDerivation rec {
+  name = "bedtools-${version}";
+  version = "2.26.0";
+
+  src = fetchFromGitHub {
+    owner = "arq5x";
+    repo = "bedtools2";
+    rev = "v${version}";
+    sha256 = "1j2ia68rmcw3qksjm5gvv1cb84bh76vmln59mvncr2an23f5a3ss";
+  };
+
+  buildInputs = [ zlib python ];
+  buildPhase = "make prefix=$out SHELL=${stdenv.shell} -j $NIX_BUILD_CORES";
+  installPhase = "make prefix=$out SHELL=${stdenv.shell} install";
+
+  meta = with stdenv.lib; {
+    description = "A powerful toolset for genome arithmetic.";
+    license = licenses.gpl2;
+    homepage = https://bedtools.readthedocs.io/en/latest/;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 12d9b13bc78..b3b78bf1827 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16970,6 +16970,8 @@ with pkgs;
     stdenv = overrideCC stdenv gcc49;
   };
 
+  bedtools = callPackage ../applications/science/biology/bedtools/default.nix { };
+
   bcftools = callPackage ../applications/science/biology/bcftools { };
 
   ecopcr = callPackage ../applications/science/biology/ecopcr { };