Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.

ABSTRACT: Shotgun 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. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application inte

SUBMITTER: Miller IJ 

PROVIDER: S-EPMC6547426 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature