ArticleBioinformatics (Oxford, England)2019
Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 59 citations in OpenAlex.
- BINSEQ: A family of high-performance binary formats for nucleotide sequences.PLoS computational biology · 2026Article
- FFC: a scalable FASTA compressor.Bioinformatics (Oxford, England) · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- FastqCA: an effective FASTQ compressor through 2D spatial redundancy reduction.Frontiers in genetics · 2026Article
- QPL-enabled HTSlib library: accelerating sequence file compression using Intel IAA.Bioinformatics advances · 2026Article
- mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing.bioRxiv : the preprint server for biology · 2025Article
- OReO: optimizing read order for practical compression.Bioinformatics advances · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- Article
- Image-centric compression of protein structures improves space savings.BMC bioinformatics · 2023Article
- AGC: compact representation of assembled genomes with fast queries and updates.Bioinformatics (Oxford, England) · 2023Article
- Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.Methods in molecular biology (Clifton, N.J.) · 2023Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- The complexity landscape of viral genomes.GigaScience · 2022Article
- MBGC: Multiple Bacteria Genome Compressor.GigaScience · 2022Article
- Article
- FASTAFS: file system virtualisation of random access compressed FASTA files.BMC bioinformatics · 2021Article
- Disk compression of k-mer sets.Algorithms for molecular biology : AMB · 2021Article
- AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models.Entropy (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryDNA 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.
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