This tool validates a FASTQ file.
This tool validates a FASTQ file. When data is paired it can also validate a pair of FASTQ files. ValidateFastq will check if the FASTQ is in valid FASTQ format. This includes checking for duplicate reads and checking whether a pair of FASTQ files contains the same amount of reads and headers match. It also check whether the quality encodings are correct and outputs the most likely encoding format (Sanger, Solexa etc.).
For documentation and manuals visit our github.io page: https://biopet.github.io/validatefastq
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install biopet-validatefastq
and update with:
conda update biopet-validatefastq
or use the docker container:
docker pull quay.io/biocontainers/biopet-validatefastq:<tag>
(see biopet-validatefastq/tags for valid values for
biopet-validatefastq is a Java program that comes with a custom wrapper shell script. By default ‘no default java option’ is set in the wrapper. The command that runs the program is ‘biopet-validatefastq’. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ‘biopet-validatefastq -Xms512m -Xmx1g’.