Simon R. Harris

This paper introduces ska lo, a reference-free variant calling tool that uses a coloured De Bruijn graph to detect SNPs, insertions, deletions, and recombination events in pathogen genomes.

This paper introduces SKA2, a method for rapid and accurate genotyping of bacterial populations, showing superior variant recall and no false positives in outbreak simulations.

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

This paper introduces a community-driven genomic resource for Neisseria gonorrhoeae that predicts antimicrobial resistance and supports public health surveillance.

This study traces the evolutionary divergence of Neisseria gonorrhoeae by analyzing global isolates, linking antimicrobial use to the emergence of two distinct lineages with different resistance strategies.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

PopPUNK provides fast, scalable clustering of bacterial genomes using k-mer analysis, enabling real-time outbreak detection and stable cluster naming across species and datasets.

Split k-mer matching lets SKA cluster and align related bacterial genomes from raw reads, matching a mapping pipeline's MRSA outbreak tree topology with nearly 17 times less CPU time.

The paper introduces a Bayesian method for dating bacterial phylogenies, leveraging precomputed phylogenetic relationships to improve speed and scalability.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.

This study evaluates the Oxford Nanopore MinION sequencer for rapid, accurate whole-genome sequencing of Neisseria gonorrhoeae, showing it can predict antimicrobial resistance and support phylogenetic analysis with optimized workflows.

Phandango provides an interactive web tool for exploring large-scale bacterial population genomics datasets by integrating multiple analysis outputs.

ARIBA rapidly identifies antimicrobial resistance genes and SNPs from sequencing reads, outperforming existing tools on bacterial datasets.

This paper introduces a high-throughput pipeline for bacterial genome assembly and improvement, demonstrating robust performance across diverse datasets and achieving high gene completeness.

SNP-sites efficiently extracts SNPs from large multi-FASTA alignments using minimal resources, enabling scalable analysis on modest hardware.