BinDash, software for fast genome distance estimation on a typical personal laptop.
basic_science · Level V
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- Record sourced from PubMed, PMID 30052763.
- Also identified by DOI 10.1093/bioinformatics/bty651.
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Abstract
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. 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. BinDash is released under the Apache 2.0 license at https://github.com/zhaoxiaofei/BinDash. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Algorithms
- Data Compression
- Genomics
- Software