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. 2019 Feb 15;35(4):671-673.
doi: 10.1093/bioinformatics/bty651.

BinDash, software for fast genome distance estimation on a typical personal laptop

XiaoFei Zhao  1
Affiliations

BinDash, software for fast genome distance estimation on a typical personal laptop

XiaoFei Zhao. Bioinformatics. .

Abstract

Motivation: The number of genomes (including meta-genomes) is increasing at an accelerating pace. In the near future, we may need to estimate pairwise distances between millions of genomes. Even with the use of cloud computing, very few softwares can perform such estimation.

Results: The multi-threaded software BinDash can perform such estimation using only a typical personal laptop. BinDash implemented b-bit one-permutation rolling MinHash with optimal densification, an existing data-mining technique. BinDash empirically outperforms the state-of-the-art software in terms of precision, compression ratio, memory usage and runtime according to our evaluation. Our evaluation is performed with a Dell Inspiron 157 559 Notebook on all bacterial genomes in RefSeq.

Availability and implementation: BinDash is released under the Apache 2.0 license at https://github.com/zhaoxiaofei/BinDash.

Supplementary information: Supplementary data are available at Bioinformatics online.

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