A practical guide to amplicon and metagenomic analysis of microbiome data
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …
field of microbiome research, and massive microbiome datasets are now being generated …
Minimum information about an uncultivated virus genome (MIUViG)
We present an extension of the Minimum Information about any (x) Sequence (MIxS)
standard for reporting sequences of uncultivated virus genomes. Minimum Information about …
standard for reporting sequences of uncultivated virus genomes. Minimum Information about …
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
A unified catalog of 204,938 reference genomes from the human gut microbiome
Comprehensive, high-quality reference genomes are required for functional characterization
and taxonomic assignment of the human gut microbiota. We present the Unified Human …
and taxonomic assignment of the human gut microbiota. We present the Unified Human …
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
Background Viruses are a significant player in many biosphere and human ecosystems, but
most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to …
most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to …
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
We previously reported on MetaBAT, an automated metagenome binning software tool to
reconstruct single genomes from microbial communities for subsequent analyses of …
reconstruct single genomes from microbial communities for subsequent analyses of …
A genomic catalog of Earth's microbiomes
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …
enabled insights into the ecology and evolution of environmental and host-associated …
A complete domain-to-species taxonomy for Bacteria and Archaea
Abstract The Genome Taxonomy Database is a phylogenetically consistent, genome-based
taxonomy that provides rank-normalized classifications for~ 150,000 bacterial and archaeal …
taxonomy that provides rank-normalized classifications for~ 150,000 bacterial and archaeal …
Oxford Nanopore R10. 4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or …
Abstract Long-read Oxford Nanopore sequencing has democratized microbial genome
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …