Software for selecting the most informative sets of genomic loci for multi-target microbial typing
High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software  Automated Selection of Typing Target Subsets (AuSeTTS) - that allows intelligent selection of optimal targets for pathogen strain typing. The objective of this software is to maximise both discriminatory power, using Simpsons index of diversity (D), and concordance with existing typing methods, using the adjusted Wallace coefficient (AW). The program interrogates molecular typing results for panels of isolates, based on large target sets, and iteratively examines each target, one-by-one, to determine the most informative subset.
software microbial typing comparative genomics multilocus sequence typing mvla binary typing mrsa cryptococcus staphylococcus aureus streptococcus pneumoniae