====== KAT ======
KAT is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.

===== Information =====

  * Version: 2.3.4
  * Added: September, 2017
  * Link: http://www.earlham.ac.uk/kat-tools

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load kat/2.3.4
$ kat --help</code>

Note that KAT supports gzip-compressed fastq files but you need to use them like this:
<code>$ kat comp -t 8 -n <(gunzip -c data_S0_L001_R1_001.fastq.gz) <(gunzip -c data_S0_L001_R2_001.fastq.gz)</code>

There are more examples for using KAT here: https://kat.readthedocs.io/en/latest/walkthrough.html

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

<code>$ cd /tmp
$ wget https://github.com/TGAC/KAT/releases/download/Release-2.3.4/kat-2.3.4.tar.gz
$ tar xf kat-2.3.4.tar.gz
$ cd kat-2.3.4
$ scl enable devtoolset-4 bash
$ module load python/3.6.2
$ sudo mkdir -p /export/apps/kat/2.3.4
$ sudo chown aorth:aorth /export/apps/kat/2.3.4
$ python -m venv /export/apps/kat/2.3.4
$ . /export/apps/kat/2.3.4/bin/activate
$ pip install -U pip setuptools
$ pip install matplotlib scipy numpy
$ ./configure --prefix=/export/apps/kat/2.3.4 --with-boost=/export/apps/boost/1.65.1
$ make -j4
$ make install
$ sudo chown -R root:root /export/apps/kat/2.3.4</code>