Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

Recent long-read assemblies often exceed the quality and completeness of available
reference genomes, making validation challenging. Here we present Merqury, a novel tool …

Immediately after birth, newborn babies experience rapid colonization by microorganisms
from their mothers and the surrounding environment. Diseases in childhood and later in life …

Population-level comparisons of prokaryotic genomes must take into account the substantial
differences in gene content resulting from horizontal gene transfer, gene duplication and …

Complete and accurate genome assemblies form the basis of most downstream genomic
analyses and are of critical importance. Recent genome assembly projects have relied on a …

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter,
presenting an untapped reservoir of microbial biodiversity and genetic resources, but has …

Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in
structuring human gut microbiomes; yet, the gut virome is far from being fully characterized …

Recovering genomes from shotgun metagenomic sequence data allows detailed taxonomic
and functional characterization of individual species or strains in a microbial community …

Profiling metagenomes against databases allows for the detection and quantification of
microorganisms, even at low abundances where assembly is not possible. We introduce …

Abstract ICEberg 3.0 (https://tool2-mml. sjtu. edu. cn/ICEberg3/) is an upgraded database
that provides comprehensive insights into bacterial integrative and conjugative elements …