Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi
Danielle J. Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A. Keane, Ayorinde O. Afolayan, Niyaz Ahmed, Saadia Andleeb, Philip Ashton, Isaac I. Bogoch, Megan E. Carey, Marie Anne Chattaway, John A. Crump, Paula Díaz, Benjamin P. Howden, , Kathryn E. Holt
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.
Genome Medicine · Oct 24, 2025Peer-reviewedMicrobiology✦ In-depth digest