Squat

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Description

SQUAT stands for Sequencing QUality Assessment Tool. It allows users to examine their sequencing data and determine if they are truly representative of the original specie based on data assessments before and after genome assemblies.

The tool aligns sequencing reads against the assembly with BWA and generates one pre-assembly and one post-assembly report at the end of the analysis.

Licence

Public

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of squat and load default version of squat as

module avail squat/ # list available modules
module load squat   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail squat

and choose explicit version you want to use.

Documentation

https://github.com/luke831215/SQUAT

Homepage

https://github.com/luke831215/SQUAT