Matchtigs: minimum plain text representation of k-mer sets.

ABSTRACT: We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 59% over unitigs and 26% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 90% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26× over unitigs and 2.10× over previous work.

SUBMITTER: Schmidt S 

PROVIDER: S-EPMC10251615 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature