PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an as-sembler that operates directly on these sketches. MSR produces...

Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.

ASHG is here in Boston, just down the street from Ginkgo's HQ.  I'm in a new role in Ginkgo Automation, trying to convince the NGS world tha...

PacBio (NASDAQ: PACB), developer of the world's most advanced sequencing technologies, today announced innovations to its Revio and Vega

Reported Tuesday, Oct 14 - 6:16am EDT (TheFly subscription required to read more.)

ASHG is here in Boston, just down the street from Ginkgo's HQ.  I'm in a new role in Ginkgo Automation, trying to convince the NGS world tha...

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.

A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

Metagenomics for Microbiology, Second Edition unveils the intricate and diverse world of microbial communities, emphasizing their critical roles in he

In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently develo...

In this study, the authors present ‘Argo’, a bioinformatics tool for identifying the host species for antibiotic resistance genes in long-read metagenomic sequence data. They validate the tool using s...