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

descriptionPublicationkeyboard_double_arrow_right Article , Other literature type , Preprint 19 Dec 2018Publisher:Cold Spring Harbor LaboratoryJournal:Bioinformatics, volume 35, pages 3,826-3,828 (issn: 1367-4803, eissn: 1367-4811,

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Authors: Kirill Kryukov; Mahoko Ueda Takahashi; So Nakagawa; Tadashi Imanishi;

doi: 10.1101/501130 , 10.1093/bioinformatics/btz144

pmid: 30799504

pmc: PMC6761962

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

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Abstract

AbstractSummaryDNA 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. NAF 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.AvailabilityNAF 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.Contactkkryukov@gmail.com

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Keywords

Base Sequence, Nucleotides, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Data Compression, Applications Notes, Algorithms, Software

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