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Dashing: Fast and Accurate Genomic Distances with HyperLogLog

View ORCID ProfileDaniel N Baker, View ORCID ProfileBen Langmead
doi: https://doi.org/10.1101/501726
Daniel N Baker
Department of Computer Science, Johns Hopkins University, 3400 N Charles St, 21218 Baltimore, USA
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  • For correspondence: dnb@cs.jhu.edu
Ben Langmead
Department of Computer Science, Johns Hopkins University, 3400 N Charles St, 21218 Baltimore, USA
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Abstract

Dashing is a fast and accurate software tool for estimating similarities of genomes or sequencing datasets. It uses the HyperLogLog sketch together with cardinality estimation methods that specialize in set unions and intersections. Dashing sketches genomes more rapidly than previous MinHash-based methods while providing greater accuracy across a wide range of input sizes and sketch sizes. It can sketch and calculate pairwise distances for over 87K genomes in under 6 minutes. Dashing is open source and available at https://github.com/dnbaker/dashing.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 20, 2018.
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Dashing: Fast and Accurate Genomic Distances with HyperLogLog
Daniel N Baker, Ben Langmead
bioRxiv 501726; doi: https://doi.org/10.1101/501726
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Dashing: Fast and Accurate Genomic Distances with HyperLogLog
Daniel N Baker, Ben Langmead
bioRxiv 501726; doi: https://doi.org/10.1101/501726

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