Jeremy Swann

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads

ReadItAndKeep removes human contamination from SARS-CoV-2 sequencing data efficiently on low-specification laptops.

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

This study optimizes Oxford Nanopore Flowcell usage for hybrid assemblies by reducing sequencing time and cost through washing steps, enabling more isolates per flowcell.

Genomic network analysis of an environmental and livestock IncF plasmid population

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

The paper develops a metagenomic metric to predict antibiotic resistance in Enterobacterales infections using pooled human faecal samples from LMICs and high-income settings.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.