Rachel Colquhoun

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

PrimalScheme: open-source community resources for low-cost viral genome sequencing

PrimalScheme provides open-source tools for designing low-cost viral genome sequencing primers, generating over 67,000 schemes and enabling large-scale genomic surveillance.

Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

The paper introduces piranha, a tool for automated detection and classification of polioviruses from nanopore sequencing reads, enabling efficient intratypic differentiation and identification of wild-type and vaccine-derived polioviruses.

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.