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

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• DNA sequence databases require efficient storage and transmission.
• Existing compression methods like gzip are widely used but can be slow for decompression.

Purpose of the Study:

• To introduce a new file format, Nucleotide Archival Format (NAF), for lossless, reference-free compression of nucleotide sequences.
• To evaluate NAF's performance against established DNA and general-purpose compression algorithms.

Main Methods:

• Developed a novel compression algorithm and file format (NAF) for FASTA and FASTQ sequences.
• Compared NAF's compression ratio and decompression speed against DELIMINATE, MFCompress, gzip, bzip2, xz, brotli, and zstd.

Main Results:

• NAF achieves compression ratios comparable to leading DNA compressors.
• NAF demonstrates significantly faster decompression speeds compared to other formats.
• The format is lossless and reference-free.

Conclusions:

• NAF provides an effective solution for compressing nucleotide sequence data.
• Its superior decompression speed makes it a valuable tool for large-scale genomic data handling.
• NAF is open-source and readily available for use.