My Project
FastqPuri, an fq quality control and filter tool

Software and source code of FastqPuri. It creates quality reports of fastq files and filters them removing low quality reads, reads containing too many N's or contamination reads (unwanted rRNA reads, impurities coming from another organism, ...).

Installation

Clone the repository, or download the source. Make sure that your system supplies the following dependencies for FastqPuri.

NOTE: FastqPuri will work without the optional dependencies but will skip creating html reports if they are not available.

$ cmake -H. -Bbuild/ [-DRSCRIPT=myRscriptexec ... ]
$ cd build
$ make

When running cmake, there are some variables you can set using the option -D followed by the variable name. This variables are,

The executables will be created in the folder bin.

WARNING: do not move the executables that depend on R scripts, anywhere else, unless you also move the corresponding R scripts respecting the local folder structure.

Executables

An exemplar work flow could be:

Documentation of the code

A Doxygen documentation of the code is available:

Contributors

Paula Pérez Rubio

License

GPL v3 (see LICENSE.txt)