Themisto is a tool designed for pseudoaligning sequence reads against a database of microbial reference genomes. The database is indexed as a colored de Bruijn graph which contains all distinct k-mers of the input genomes. Each k-mer is annotated with a set of colors, where the colors describe which species or strains contain the given k-mer. For more information, see our preprint.
The tool is available at https://github.com/algbio/Themisto