kat-software
Table of Contents
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
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 11:52 by aorth