Ajit Lalvani

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.

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

fastlin rapidly and accurately types Mycobacterium tuberculosis complex lineages from sequencing data, detecting mixed-lineage strains and estimating proportions.

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