Sync paired-end FASTQ files. Some QC tools are not aware of paired-end sequencing. These tools often delete one read of the read pair, while leaving the other. This will lead to the FASTQ files for the reads being out of sync.

FastqSync will check back with the original FASTQ files (before QC) and make sure that when a read is removed from one pair, the other read from the pair is also removed.


FastqSync 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 FastqSync here. To generate the usage run:

java -jar <FastqSync_jar> --help


The tool requires two FASTQ files,two output FASTQ file and the original FASTQ files.

This tool works with gzipped or non-gzipped FASTQ files. The output file will be gzipped when the input is also gzipped.


To sync two fastq files:

java -jar <FastqSync_jar> \
--in1 read1.fastq \
--in2 read2.fastq \
--ref1 beforeQC_read1.fastq \
--ref2 beforeQC_read2.fastq \
--out1 output1.fastq \
--out2 output2.fastq


Usage for FastqSync:

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
--ref1, -r yes no Reference R1 FASTQ file
--ref2 yes no Reference R2 FASTQ file
--in1, -i yes no Input FASTQ file 1
--in2, -j yes no Input FASTQ file 2
--out1, -o yes no Output FASTQ file 1
--out2, -p yes no Output FASTQ file 2


FastqSync 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 BIOPET pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


The source code of FastqSync can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

FastqSync is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on FastqSync. We have had good results with this IDE.


For any question related to FastqSync, please use the github issue tracker or contact the SASC team directly at: