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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 distinctdoi:10.1101/130997 fatcat:a4xzz3vf4vaghaplsqmygcs6ni