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KAT

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

Information

Usage

See versions of kat which are available:

$ module avail kat

Load one version into your environment and run it:

$ module load kat/2.3.4
$ kat --help

Note that KAT supports gzip-compressed fastq files but you need to use them like this:

$ kat comp -t 8 -n <(gunzip -c data_S0_L001_R1_001.fastq.gz) <(gunzip -c data_S0_L001_R2_001.fastq.gz)

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

Installation

Notes from the sysadmin during installation:

$ 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
kat-software.txt · Last modified: 2017/09/27 14:52 by aorth