Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes

Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C.

doi:10.1101/251462

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bioRxiv · 10.1101/251462

Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes

Miller, I. J.·Rees, E. R.·Ross, J.·Miller, I.·Baxa, J.·Lopera, J.·Kerby, R. L.·Rey, F. E.·Kwan, J. C.

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Abstract

MotivationShotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of \"binning\" where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. Existing methods, however, suffer from: (1) reliance on human pattern recognition, which is inherently unscalable; (2) requirement for multiple co-assembled metagenomes, which degrades assembly quality due to strain variance; and (3) assumption of prior host genome removal not feasible for non-model hosts. We therefore devised a fully-automated pipeline, termed \"Autometa,\" to address these issues. Results: Autometa implements a method for taxonomic partitioning of contigs based on predicted protein homology, and this was shown to vastly improve binning in host-associated and complex metagenomes. Autometas method of automated clustering, based on Barnes-Hut Stochastic Neighbor Embedding (BH-tSNE) and DBSCAN, was shown to be highly scalable, outperforming other binning pipelines in complex simulated datasets.\n\nAvailability and implementationAutometa is freely available at https://bitbucket.org/jasonckwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).\n\nContactjason.kwan@wisc.edu\n\nSupplementary informationSupplementary data are available attached to this article at https://biorxiv.org

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Miller, I. J., Rees, E. R., Ross, J., Miller, I., Baxa, J., Lopera, J., Kerby, R. L., Rey, F. E., Kwan, J. C.. 2018-01-22. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. https://doi.org/10.1101/251462

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