2019/02/22 by Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa +1 · 1 voice · 4 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #DNA and Biological Computing #Genomics and Phylogenetic Studies
paper · pdf · doi:10.1093/bioinformatics/btz144
openalex publication_date 2019/02/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/11
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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 INFORMATION: Supplementary data are available at Bioinformatics online.