ArticleNucleic acids research2019
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Integration of multiple metabolic pathways supports high rates of carbon precipitation in living microbialites.Nature communications · 2025Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- An Assessment of Chemical Diversity in Microbial Natural Products.ACS central science · 2025Review
- Jaspamide/Jasplakinolide Is Synthesized byJournal of natural products · 2025Article
- Article
- Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.NPJ biofilms and microbiomes · 2025Article
- A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont.Environmental microbiology · 2025Article
- Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.mBio · 2025Article
- Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria.eLife · 2025Article
- Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.Applied and environmental microbiology · 2024Article
- Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.BMC microbiology · 2024Article
- Article
- Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.bioRxiv : the preprint server for biology · 2024Article
- Prevalence and diversity of TAL effector-like proteins in fungal endosymbioticMicrobial genomics · 2024Article
- Short macrocyclic peptides in sponge genomes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.Urolithiasis · 2024Article
- Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.The ISME journal · 2024Article
- Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring.The ISME journal · 2024Article
- The polyketide to fatty acid transition in the evolution of animal lipid metabolism.Nature communications · 2024Article
- Artificial intelligence for natural product drug discovery.Nature reviews. Drug discovery · 2023Review
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Authors and funding
9 authors.
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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 integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https://bitbucket.org/jason_c_kwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.