====== hypo ======
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.

===== Information =====

  * Version: 1.0.3
  * Added: January, 2021
  * Link: https://github.com/kensung-lab/hypo

===== Usage =====

See versions of hypo which are available:
<code>$ module avail hypo</code>

Load one version into your environment and run it:
<code>$ module load hypo/1.0.3
$ hypo</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

**Note:** I had to modify the CMakeLists.txt file to hard code our global htslib, see: https://github.com/kensung-lab/hypo/issues/23