Summary of available workflows in //keeSeek//

There are four available ways to start keeSeek:

• “Default” mode (-w option): the user sets a desired length and keeSeek proceeds with an ordered generation of all existing k-mers of that length;
• “Anagram” mode (-a option): the user chooses an exact nucleotide composition and keeSeek generates all possible anagrams with that nucleotide content;
• “single” mode (-s option): the user can verify a single sequence providing it from command line;
• “Input File” mode (-i option): the user can verify a file containing a list of sequences.

After this initial step, sequences that are 18-24 nt long are analyzed and possibly discarded when they do not possess primer-like features (this step is optional and can be disabled with –z option). Before searching the candidate k-mers vs. the reference sequence the user can choose to apply a reshuffling mask to increase the variability of the results (-R option). Finally, neverwords are given in output, ordered by decreasing number of mismatches.