Virtual seminar : “Improved metagenome binning and assembly using deep variaQonal autoencoders”

EVENT : C3BI Seminars

Main speaker : Simon RASMUSSEN, from Technical University of Denmark and Novo Nordisk Foundation Center for Protein Research University of Copenhagen Date : 07-01-2021 at 10:00 am Location : Teams (e-seminars) ,Institut Pasteur, Paris

Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop Variational Autoencoders for Metagenomic Binning (VAMB), a program that uses deep variational autoencoders to encode sequence co-abundance and k-mer distribution information prior to clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any prior knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29–98% and 45% more near-complete genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% ANI and reconstructed 255 and 91 near complete Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 near-complete bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at


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