Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,822 bioRxiv papers from 266,142 authors.
Binning microbial genomes using deep learning
Jakob Nybo Nissen,
Casper Kaae Sonderby,
Jose Juan Almagro Armenteros,
Christopher Heje Groenbech,
Henrik Bjorn Nielsen,
Thomas Nordahl Petersen,
Posted 10 Dec 2018
bioRxiv DOI: 10.1101/490078
Posted 10 Dec 2018
Identification and reconstruction of microbial species from metagenomics wide genome sequencing data is an important and challenging task. Current existing approaches rely on gene or contig co-abundance information across multiple samples and k-mer composition information in the sequences. Here we use recent advances in deep learning to develop an algorithm that uses variational autoencoders to encode co-abundance and compositional information prior to clustering. We show that the deep network is able to integrate these two heterogeneous datasets without any prior knowledge and that our method outperforms existing state-of-the-art by reconstructing 1.8 - 8 times more highly precise and complete genome bins from three different benchmark datasets. Additionally, we apply our method to a gene catalogue of almost 10 million genes and 1,270 samples from the human gut microbiome. Here we are able to cluster 1.3 - 1.8 million extra genes and reconstruct 117 - 246 more highly precise and complete bins of which 70 bins were completely new compared to previous methods. Our method Variational Autoencoders for Metagenomic Binning (VAMB) is freely available at: https://github.com/jakobnissen/vamb
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