Martin Hunt

Flex-It: A global standardised genotyping framework for Shigella flexneri

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.

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.

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

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.

Rapidly and reproducibly building a comprehensive catalogueof resistance-associated variants for M. tuberculosis

This paper develops an automated method to build a comprehensive catalogue of resistance-associated variants for M. tuberculosis, achieving comparable performance to existing catalogues without expert rules.

Complete genomes reveal the full extent of Mycobacterium tuberculosis complex diversity across evolutionary scales

The paper uses long-read sequencing to generate complete genomes of Mycobacterium tuberculosis complex isolates, revealing increased genomic diversity and improved resolution in transmission analysis.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

Hostile: accurate host decontamination of microbial sequences

Hostile is a tool for removing human host sequences from microbial sequencing data, achieving high accuracy in read removal while preserving target microbial sequences.

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

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

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Minos integrates variant calls from multiple tools to adjudicate discrepancies and jointly genotype bacterial cohorts, improving accuracy in detecting SNPs and indels.

Nucleotide-resolution bacterial pan-genomics with reference graphs

This paper introduces a pan-genome graph structure and software tool, pandora, to analyze bacterial genomic variation across multiple isolates with higher SNP recovery and lower error rates than existing methods.

Enabling multiscale variation analysis with genome graphs

The paper introduces a genome graph model and software to genotype multiscale genetic variation across different sequence backgrounds, demonstrating applications in tuberculosis and malaria genomes.

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

Inferring synteny between genome assemblies: a systematic evaluation

The paper evaluates how draft genome assemblies affect synteny analysis and finds that fragmented assemblies can lead to significant underestimation of synteny and unreliable downstream results.

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

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

Comparison of bacterial genome assembly software for MinION data

The paper compares bacterial genome assembly software for MinION data, finding Canu provides the most accurate assembly while Miniasm is fastest.

Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data

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

Circlator: automated circularization of genome assemblies using long sequencing reads

Circlator automates genome circularization using long reads, accurately circularizing 26 of 27 test sequences from bacteria and other organisms.

Roary: Rapid large-scale prokaryote pan genome analysis

Roary builds large-scale prokaryote pan genomes efficiently, identifying core and dispensable accessory genes using a single CPU in under 5 hours.