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

ABSTRACT:

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 decompresso

SUBMITTER: Kryukov K 

PROVIDER: S-EPMC6761962 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature