The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …

Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles …

Bacteriophages have important roles in the ecology of the human gut microbiome but are
under-represented in reference databases. To address this problem, we assembled the …

Comprehensive, high-quality reference genomes are required for functional characterization
and taxonomic assignment of the human gut microbiota. We present the Unified Human …

… Next, we evaluated CheckV’s accuracy in detecting host contamination on provirus
sequences (Supplementary Table 8). To generate mock proviruses, we identified 382 …

The genome sequences of many species of the human gut microbiome remain unknown,
largely owing to challenges in cultivating microorganisms under laboratory conditions. Here …

… on similarity to viral proteins from NCBI’s NR (retrieved in 2022-05-19), we used MMseqs2’s
(version 13.45111) (27) taxonomy module with the ‘- -start-sens 4 -s 6 - -sens-steps 2’ …

We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an
integrated computational pipeline for quantifying bacterial species abundance and strain-…

… (s) if available at the genus rank, match to CRISPR spacer(s) if available at the genus rank,
match to host genome(s) if available above the genus rank, match to CRISPR spacer(s) if …

… Different computational approaches are available to predict the host(s) of uncultivated viruses
based on their genome sequences, but thus far individual approaches are limited either in …