Fastqvalidator tool validates the fastq files and prints out errors. For eg. one of my files, for some reason, had more quality values than the bases in a read due to which downstream processes were failing. Installation requirements are taken from https://github.com/statgen/fastQValidator and https://github.com/statgen/libStatGen.
Assuming that user has sudo/ root privileges, please follow the procedure as given below:
- Install statgen dependencies as outlined in https://github.com/statgen/libStatGen
sudo apt-get install g++ libssl-dev zlib1g-dev - Then download libStatgen source file as zip (from clone or download option on github page)
- Unzip the source and type 'sudo make'
- This would compile the necessary files
- Download fastqvalidator source file from github (https://github.com/statgen/fastQValidator) as zip file (from clone or download option on github)
- Unzip the source
- Replace the libstatgen folder with folder from step 4 i.e replace libstatgen provided by fastqvalidator with compiled libstatgen folder from step 4
- Within, fastqvalidator folder, type "sudo make". This would compile and creates a folder named "fastQValidator". Within fastQValidator folder, bin would be present where fastqvalidator binary is kept. Add this path to your system/user path.