diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix
new file mode 100644
index 000000000000..9ccf54a81133
--- /dev/null
+++ b/pkgs/applications/science/biology/hisat2/default.nix
@@ -0,0 +1,49 @@
+{stdenv, fetchurl, unzip, which, python}:
+
+stdenv.mkDerivation rec {
+  name = "hisat2-${version}";
+  version = "2.1.0";
+
+  src = fetchurl {
+    url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
+    sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
+  };
+
+  buildInputs = [ unzip  which python ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp hisat2 \
+       hisat2-inspect-l \
+       hisat2-build-s \
+       hisat2-align-l \
+       hisat2-inspect \
+       hisat2-align-s \
+       hisat2-inspect-s \
+       hisat2-build-l \
+       hisat2-build \
+       extract_exons.py \
+       extract_splice_sites.py \
+       hisat2_extract_exons.py \
+       hisat2_extract_snps_haplotypes_UCSC.py \
+       hisat2_extract_snps_haplotypes_VCF.py \
+       hisat2_extract_splice_sites.py \
+       hisat2_simulate_reads.py \
+       hisatgenotype_build_genome.py \
+       hisatgenotype_extract_reads.py \
+       hisatgenotype_extract_vars.py \
+       hisatgenotype_hla_cyp.py \
+       hisatgenotype_locus.py \
+       hisatgenotype.py \
+       $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Graph based aligner";
+    license = licenses.gpl3;
+    homepage = https://ccb.jhu.edu/software/hisat2/index.shtml;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = [ "x86_64-linux" "i686-linux" ];
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f48704cc514d..40440f1b379f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -20641,6 +20641,8 @@ with pkgs;
 
   ezminc = callPackage ../applications/science/biology/EZminc { };
 
+  hisat2 = callPackage ../applications/science/biology/hisat2 { };
+
   htslib = callPackage ../development/libraries/science/biology/htslib { };
 
   igv = callPackage ../applications/science/biology/igv { };