Despite the accelerating number of uncultivated virus sequences discovered in
metagenomics and their apparent importance for health and disease, the human gut virome …

Due to technical limitations, most gut microbiome studies have focused on prokaryotes,
overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the …

Despite recent advances in metagenomic binning, reconstruction of microbial species from
metagenomics data remains challenging. Here we develop variational autoencoders for …

Motivation Although the set of currently known viruses has been steadily expanding, only a
tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic …

Background Prokaryotic viruses referred to as phages can be divided into virulent and
temperate phages. Distinguishing virulent and temperate phage–derived sequences in …

Background Identifying viral sequences in mixed metagenomes containing both viral and
host contigs is a critical first step in analyzing the viral component of samples. Current tools …

Metagenomics enables the reconstruction of microbial genomes in complex microbial
communities without the need for culturing. Since assembly typically results in fragmented …

The human gut microbiome has been extensively explored, while the archaeal viruses
remain largely unknown. Here, we present a comprehensive analysis of the archaeal …

Background Viruses are central to microbial community structure in all environments. The
ability to generate large metagenomic assemblies of mixed microbial and viral sequences …

Genome binning has been essential for characterization of bacteria, archaea, and even
eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed …