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KungFq | An approach to compress fastq files

Compresses FASTQ files, decompress them and access single reads in the compressed ones. KungFQ is based on dividing the reads in blocks and superblocks and computes statistics over each superblocks in order to be able to summarize common parts of them. For sequences, it allows characters different from A, C, T, G, and N considering the rare occurrences of IUPAC codes moving their encoding in the quality streams. It reaches good compression levels on base space fastq files : the tool should be useful for those who need to reduce the space required to store high quantity of next generation sequencing data.

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KungFq classification

KungFq specifications

Unique identifier:
Command line interface
Input data:
RNA or DNA sequences
Output format:
Programming languages:
Computer skills:
Software type:
Restrictions to use:
Input format:
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0

KungFq distribution


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Department of Genetics, Biology and Biochemistry, Molecular Biotechnology Center, Torino, Italy; DNDG srl, Torino, Italy

Funding source(s)

This work was funded by Italian Ministry of University and Research FIRB piattaforme/reti rbpr05zk2z_006.

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