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

Ingle DJ, Hawkey J, Hunt M, Iqbal Z, Keane JA, Afolayan AO, Ahmed N, Andleeb S, Ashton PM, Bogoch II, Carey ME, Chattaway MA, Crump JA, Guevara PD, Howden BP, Izumiya H, Jacob JJ, Judd LM, Kapil A, Keddy KH, Kim JY, Levine MM, Morita M, Nair S, Octavia S, Okeke IN, Osadebamwen PE, Rahman SIA, Rokney A, Rasko DA, Shamanna V, Sikorski MJ, Smith AM, Sunmonu GT, Tagg KA, Wick RR, Dyson ZA, Holt KE, Global Typhoid Genomics Consortium,