HyPo–a Hybrid Polisher– utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments. As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assembly in about one-third time with about half the memory requirements in comparison to contemporary widely used polishers like Racon.
See versions of hypo which are available:
$ module avail hypo
Load one version into your environment and run it:
$ module load hypo/1.0.3 $ hypo
Notes from the sysadmin during installation:
$ cd /tmp $ git clone --recursive https://github.com/kensung-lab/hypo.git -b v1.0.3 $ cd hypo # Install a newer compiler for C++17 features in hypo $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ $ scl enable devtoolset-7 bash $ mkdir build $ cd build $ cmake3 -DCMAKE_BUILD_TYPE=Release .. $ make -j4 $ sudo mkdir -p /export/apps/hypo/1.0.3/bin $ sudo cp bin/hypo /export/apps/hypo/1.0.3/bin
Note: I had to modify the CMakeLists.txt file to hard code our global htslib, see: https://github.com/kensung-lab/hypo/issues/23