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METHODS article

Front. Microbiol.
Sec. Microbiotechnology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1521181

dna2bit: High Performance Genomic Distance Estimation Software for Microbial Genome Analysis

Provisionally accepted
Juzeng Li Juzeng Li Yuxin Tian Yuxin Tian Yi Wang Yi Wang *Jin Li Jin Li *
  • Fudan University, Shanghai, China

The final, formatted version of the article will be published soon.

    dna2bit is an ultra-fast software specifically engineered for microbial genome analysis, particularly adept at calculating genome distances within metagenome and single amplified genome datasets. Distinguished from existing software such as Mash and Dashing, dna2bit employs feature hashing technique and Hamming distance to achieve enhanced speed and memory utilization, without sacrifice in the accuracy of ANI calculations. dna2bit has promising applications in various domains such as ANI approximation, metagenomic sequence clustering, and homology querying. dna2bit significantly boosts computational efficiency in handling large datasets including Single Amplified Genomes (SAGs), thereby facilitating a better understanding of the population heterogeneity and comparative genomics of microorganisms. dna2bit is available at https://github.com/lijuzeng/dna2bit.

    Keywords: Hamming distance, Average nucleotide identity, Genome distance, metagenomes clustering, single amplified genomes

    Received: 01 Nov 2024; Accepted: 10 Dec 2024.

    Copyright: © 2024 Li, Tian, Wang and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Yi Wang, Fudan University, Shanghai, China
    Jin Li, Fudan University, Shanghai, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.