Ryan R. Wick

The paper benchmarks preprocessing pipelines for Oxford Nanopore reads in bacterial genomics, finding that no single approach optimally balances variant calling and assembly performance across all metrics.

The paper analyzes bacterial diversity and strain dynamics in the infant respiratory microbiome using whole genome sequencing and metagenomics, revealing age-dependent shifts in dominant taxa and expanding reference genomes for airway microbes.

The paper benchmarks six long-read simulators against Oxford Nanopore WGS data, finding PBSIM3 best reproduces read-level properties but none capture all error features.

Verticall detects recombination in bacterial genomic datasets, outperforming existing tools on large and diverse datasets.

Flex-It is a genotyping framework for S. flexneri that rapidly characterizes genotypes and resistance determinants from sequencing data, enabling standardized surveillance of its population structure and antimicrobial resistance.

agtools provides a Python framework to manipulate assembly graphs across formats, enabling analysis and integration into bioinformatics workflows.

This study identifies linear plasmids in six Rhizobiaceae strains, revealing their presence in nonpathogenic and plant tumorigenic bacteria and suggesting they may be more widespread than previously thought.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

The paper benchmarks 44 tools for plasmidome reconstruction from short-read assemblies in Klebsiella pneumoniae, finding PlaScope and MOB-suite as top performers.

The paper develops a TraDIS platform for Enterococcus faecium using nanopore sequencing and a WebAssembly tool to study vancomycin resistance and persistence.

Amira detects AMR genes directly from long reads using gene-space de Bruijn graphs, achieving high recall and accuracy compared to assembly-based methods.

This study evaluates variant calling from bacterial genome assemblies versus read-based methods, finding that assembly-based approaches require error-free assemblies to achieve high accuracy.

This study analyzes KpSC populations across human, animal, and marine sources in Norway, showing distinct yet overlapping populations with limited recent transmission between niches.

This paper reports the complete genome of Candidatus Paracoxiella cheracis, revealing insights into its pathogenesis and phylogeny within the Coxiellaceae family.

This paper compares strict and soft core SNP filtering strategies for bacterial phylogenetics, showing soft cores retain more informative sites and improve phylogenetic accuracy.

This paper demonstrates that CRISPR-Cas9 enrichment combined with Oxford Nanopore sequencing improves detection of AMR genes and MLST in patient samples compared to unenriched sequencing.

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

This study benchmarks variant callers on bacterial nanopore data, finding deep learning tools outperform traditional methods and Illumina in accuracy and efficiency.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

The paper analyzes the genetic diversity and functionality of rmpADC variants in Klebsiella pneumoniae to understand their role in virulence and antimicrobial resistance.

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

The paper introduces FMLRC2, a tool for polishing de novo nanopore assemblies, and demonstrates its effectiveness for bacterial and eukaryotic genomes.

This study evaluates ONT-only assemblies for genomic surveillance of Klebsiella pneumoniae, showing reliable MLST, K type, and AMR detection but challenges in cluster detection.

The paper identifies a plasmid (Plasmid A) that transmitted four times into different Klebsiella lineages, causing 50% of ESBL episodes and persisting for 3-6 years, contributing to 21% of ESBL+ infections.

Polypolish improves bacterial genome assemblies by fixing repeat region errors using short-read data, outperforming existing tools when combined with others.

Kaptive 2.0 updates capsule and LPS locus typing for Klebsiella pneumoniae by adding novel sequences and improving O2 antigen prediction, enabling better surveillance and control strategies.

Trycycler improves bacterial genome assemblies by combining multiple long-read assemblies, reducing errors and improving accuracy when followed by polishing with Medaka and Pilon.

This study compares Oxford Nanopore ligation and rapid library preparation methods for bacterial genome sequencing, finding that rapid methods better recover small plasmids.

This study presents the Ostreobium nuclear genome and metatranscriptomic analysis to understand its adaptations to the coral skeleton environment and its role in coral holobiont dynamics.