SeqStats outputs several stats on a FASTQ file.

Outputted stats:

  • Bases
  • Total number
  • Base qualities, with the number of bases having that quality
  • Number of each nucleotide
  • Reads
  • Total number
  • Number of reads with 'N' bases
  • minimum length
  • maximum length
  • A histogram of the average base qualities
  • The quality encoding (Sanger, solexa etc.)
  • A histogram of the read lengths.


SeqStat 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 SeqStat here. To generate the usage run:

java -jar <SeqStat_jar> --help


By default stats are outputted to stdout in json format. If an output file is specified it writes to the file in json format.


To run SeqStat and save the output in a JSON file:

java -jar <SeqStat_jar> \
-i input.fastq \
-o output.json

To run SeqStat and wirte the output to stdout:

java -jar <SeqStat_jar> \
-i input.fastq


Usage for SeqStat:

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
--fastq, -i yes no FastQ file to generate stats from
--output, -o no no File to write output to, if not supplied output go to stdout


SeqStat 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 SeqStat can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

SeqStat 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 SeqStat. We have had good results with this IDE.


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