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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:
OMICS_00962
Interface:
Command line interface
Input data:
RNA or DNA sequences
Output format:
GZIP, LZMA
Programming languages:
C++
Computer skills:
Advanced
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTQ
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Stability:
Stable

KungFq distribution

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Publications

Institution(s)

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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