Optimization of a fragment size analysis tool for identification of Cryptosporidium species and Gp60 alleles infecting domestic ruminants.

•A capillary electrophoresis (CE) fragment size analysis tool is optimized.•The CE tool differentiates most common Cryptosporidium species infecting ruminants.•Most GP60 subtypes within IIa and IId families are differentiated by the CE tool.•The CE tool is a discriminatory and time/cost-saving alternative to sequencing.