Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particular, Tallymer was used to index a set whole genome shotgun sequences from maize (B73) (total size 109 bp).
Tallymer was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available.
A manual can be found here.
