Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

Bioinformatics
Kirill KryukovTadashi Imanishi

Abstract

DNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF)-a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. Nucleotide Archival Format compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli and zstd. NAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use. Supplementary data are available at Bioinformatics online.

References

Jul 27, 2012·Bioinformatics·Monzoorul Haque MohammedSharmila S Mande
Oct 18, 2013·Bioinformatics·Armando J Pinho, Diogo Pratas
Dec 14, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anas Al-OkailyChun-Hsi Huang

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Citations

Jan 19, 2020·Scientific Reports·Sebastian Deorowicz
Nov 13, 2020·GigaScience·Milton SilvaArmando J Pinho
Jan 10, 2021·Trends in Genetics : TIG·Alice M Kaye, Wyeth W Wasserman
Nov 3, 2021·BMC Bioinformatics·Youri HoogstrateHarmen J G van de Werken
Oct 1, 2021·Journal of Bioinformatics and Computational Biology·Winfield Chen, Lloyd T Elliott
Jan 28, 2022·GigaScience·Szymon Grabowski, Tomasz M Kowalski

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Software Mentioned

gzip
zstd
MFCompress
DELIMINATE

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