Work

dna2bit: high performance genomic distance estimation software for microbial genome analysis

Year: 2024

Type: article

Abstract: 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 average nucleotide identity calculations. dna2bit has promising applications in various domains such as average nucleotide identity approximation, metagenomic sequence clustering, and homology querying. dna2bit significantly boosts computational efficiency in handling large datasets including single amplified genomes, thereby facilitating a better understanding of the population heterogeneity and comparative genomics of microorganisms. dna2bit is available at https://github.com/lijuzeng/dna2bit.

Source: Frontiers in Microbiology

DOI: 10.3389/fmicb.2024.1521181

Authors: Juzeng Li, Yuxin Tian, Yi Wang, Li Jin

Institutions: Fudan University, State Key Laboratory of Genetic Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,295

Funders: National Natural Science Foundation of China, Fudan University