Table 1. Terminology.

Summary of key technical terms used in this article.

Term	Description
k-mer	String of length k.
Submer	Substring of length k (that is, a k-mer) selected from a longer string by a submer rule.
Submer rule	Algorithm for selecting a subset of k-mers in a string. If a k-mer at a given position in the string is selected, it is a submer, otherwise it is not a submer.
Context-free submer rule	Submer rule which considers only the k-mer sequence. All submer rules considered here are context-free except minimizers.
Context-dependent submer rule	Submer rule which considers one or more flanking letters in addition to the k-mer sequence. Minimizers are the only submers of this type considered here.
Coding function	Function which takes a k-mer sequence as input and reports an integer as output.
k-mer code	Integer value for the k-mer reported by a coding function.
k-mer order	Function which takes two k-mers as input and returns a boolean true/false value. This can be interpreted as a greater-than-or-equal operator. A coding function can be used to define a k-mer order, for example, by applying >= to codes.
Minimizer	Submer rule which selects a k-mer if it has the smallest code in any of the windows of w consecutive k-mers in which it appears.
Modulo submer	Submer rule which selects a k-mer if its integer code is zero modulo c, where c is an integer parameter of the rule.
Mincode submer	Submer rule which selects a k-mer if its code is less than H/c, where H is the maximum possible code and c is a real-valued parameter of the rule.
Universal Hitting Set (UHS)	A set of k-mer sequences such that at least one member of the set must be found in any sequence of length w.
Syncmer	A family of submer rules which select a k-mer based on the position of its smallest s-mer.