Program acronym : cq2ip33fq

Despite some free tools on the web claim to do a translation of the 'ColorSpace' and 'Quality' files of the next generation sequencing machines of ThermoFisherScientific/ LifeTechnology/ ABI 5500xl and derivatives to the established and free 'FASTQ' data format, all the existing tools are failing in one or another aspect (e.g. solid2fastq.pl was introducing errors in 2015).
To fill this gap a fast C++ tool was developed which is taking a colorspace fasta file and a colorspace quality fasta file. The result is a true Pred33 (Illumina) conforming fastq fileformat. Both files need to have a corresponding read name structure / identical order.

The C++ boost libraries should be installed on the system for this program to work (Debian: sudo apt install libboost-all-dev). This program was tested on Linux - Debian.

cq2ip33fq : the readme file [02.10.2015] , the binary, source code, Eclipse workspace, and test files.

Program acronym : TransformCGH3

The CGH data parser transforms the exported ASCII raw data from an Applied Imaging system v.3.01 (from 1995) in a vector like format usable to be easily imported in e.g. R or LibreOffice.
Optional the blanking of the centromer and none evaluable regions might be performed during the conversion process.

Details / Download [14.10.2003]

Program acronym : colorQ2baseQ

The program is taking a regular fastq format file, where the second line is a colorspace format line while the fourth line is already a true Phred33 conforming quality score line. The colorspace will be converted into basespace and the (first) anchor base of the colorspace and the corresponding quality score will be removed - so the length is minus one. The result is a true base space fastq fileformat.

The C++ boost libraries should be installed on the system for this program to work (Debian: sudo apt install libboost-all-dev). This program was tested on Linux - Debian.

colorQ2baseQ : the binary [30.09.2020] , source code, Eclipse workspace, and a minimal test file.