:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...

Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...

Abstract. The widespread adoption of high-throughput sequencing technologies and multi-omics approaches has led to rapid accumulation of genomic, transcrip

Turning "cold" tumors "hot"

Scientific Data - Complete genome sequencing of 18 urea-utilizing Vibrio strains isolated from coral

Background Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbio...

This study evaluates the suitability of Oxford Nanopore Technologies R10 sequencing for core-genome multi-locus sequence typing (cgMLST), a widely used method in (clinical) outbreak investigation and ...

Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs. Results We present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes. Conclusions SVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.

In this work, authors tracked a pneumococcal serotype 3 strain persisting for a year in a healthy adult, revealing limited genetic change but stable multidrug resistance and features linked to vaccine escape.