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GATTACA: Lightweight Metagenomic Binning with Compact Indexing of Kmer Counts and MinHash-based Panel Selection

Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
doi: https://doi.org/10.1101/130997
Victoria Popic
1Department of Computer Science, Stanford University, Stanford CA, USA
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Volodymyr Kuleshov
1Department of Computer Science, Stanford University, Stanford CA, USA
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Michael Snyder
2Department of Genetics, Stanford University, Stanford CA, USA
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Serafim Batzoglou
1Department of Computer Science, Stanford University, Stanford CA, USA
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Abstract

We introduce GATTACA, a framework for rapid and accurate binning of metagenomic contigs from a single or multiple metagenomic samples into clusters associated with individual species. The clusters are computed using co-abundance profiles within a set of reference metagnomes; unlike previous methods, GATTACA estimates these profiles from k-mer counts stored in a highly compact index. On multiple synthetic and real benchmark datasets, GATTACA produces clusters that correspond to distinct bacterial species with an accuracy that matches earlier methods, while being up to 20× faster when the reference panel index can be computed offline and 6× faster for online co-abundance estimation. Leveraging the MinHash technique to quickly compare metagenomic samples, GATTACA also provides an efficient way to identify publicly-available metagenomic data that can be incorporated into the set of reference metagenomes to further improve binning accuracy. Thus, enabling easy indexing and reuse of publicly-available metagenomic datasets, GATTACA makes accurate metagenomic analyses accessible to a much wider range of researchers.

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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-NC 4.0 International license.
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Posted April 26, 2017.
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GATTACA: Lightweight Metagenomic Binning with Compact Indexing of Kmer Counts and MinHash-based Panel Selection
Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
bioRxiv 130997; doi: https://doi.org/10.1101/130997
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GATTACA: Lightweight Metagenomic Binning with Compact Indexing of Kmer Counts and MinHash-based Panel Selection
Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
bioRxiv 130997; doi: https://doi.org/10.1101/130997

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