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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 -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:

hypo-software.txt · Last modified: 2021/01/06 15:31 by aorth