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.).
ValidateFastq requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.
Download the latest version of ValidateFastq here. To generate the usage run:
java -jar <ValidateFastq_jar> --help
ValidateFastq validates the following things:
To validate a fastq file use:
java -jar <ValidateFastq_jar> \ -i input.fastq
To validate a pair of fastq files use:
java -jar <ValidateFastq_jar> \ -i input.fastq \ -j input2.fastq
Usage for ValidateFastq:
|Option||Required||Can occur multiple times||Description|
|--log_level, -l||no||no||Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'|
|--help, -h||no||no||Print usage|
|--version, -v||no||no||Print version|
|--fastq1, -i||yes||no||FASTQ file to be validated. (Required)|
|--fastq2, -j||no||no||Second FASTQ to be validated if FASTQs are paired. (Optional)|
|--disableFail||no||no||Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0|
ValidateFastq is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.
ValidateFastq is build using sbt. Before submitting a pull request, make sure all tests can be passed by
sbt test from the project's root. We recommend using an IDE to work on ValidateFastq. We have had
good results with this IDE.