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Related Experiment Video

Updated: Sep 5, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.

Kirill Kryukov¹, Lihua Jin², So Nakagawa³

¹Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

Patterns (New York, N.Y.)

|July 12, 2022

Summary

Nucleotide Archival Format (NAF) significantly speeds up downloading SARS-CoV-2 genome data from major databases. This new compression method offers substantial improvements in efficiency, saving time and resources for researchers worldwide.

Keywords:

GISAID Global Initiative on Sharing Avian Flu Data INSDC International Nucleotide Sequence Database Collaboration NAF Nucleotide Archival Format SARS-CoV-2 genome database sequence data compression

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate SARS-CoV-2 genome data is crucial for epidemiology, vaccine development, and variant tracking.
Millions of SARS-CoV-2 genomes have been sequenced, but downloading them from databases is inefficient.
Current compression methods for genomic data are suboptimal, leading to slow and unreliable downloads.

Purpose of the Study:

To evaluate available compression methods for SARS-CoV-2 genome data.
To introduce and demonstrate the effectiveness of the Nucleotide Archival Format (NAF).
To provide a tutorial for installing and using NAF.

Main Methods:

Comparative analysis of various compression algorithms for genomic data.
Performance evaluation of NAF against existing methods (gzip, xz, uncompressed FASTA) across different databases (GISAID, DDBJ, GenBank, ENA).

Main Results:

NAF demonstrated significant efficiency gains: 52.2x for gzip-compressed GISAID data, 3.7x for xz-compressed GISAID data.
NAF improved throughput by 40x for gzip-compressed DDBJ data.
NAF accelerated data distribution by 29.3x compared to uncompressed FASTA for GenBank and ENA.

Conclusions:

NAF offers a substantial improvement in compression efficiency for SARS-CoV-2 genome data.
Implementing NAF in sequence databases would save time, bandwidth, and disk space.
Adoption of NAF would accelerate biological and medical research globally.