Matchtigs: minimum plain text representation of kmer sets

Schmidt, S.; Khan, S.; Alanko, J.; Tomescu, A. I.

doi:10.1101/2021.12.15.472871

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bioRxiv · 10.1101/2021.12.15.472871

Matchtigs: minimum plain text representation of kmer sets

Schmidt, S.·Khan, S.·Alanko, J.·Tomescu, A. I.

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Abstract

We propose a polynomial algorithm computing a minimum plain-text representation of kmer 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 60% over unitigs and 27% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 91% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26x over unitigs and 2.10x over previous work. Availabilitymatchtigs: https://github.com/algbio/matchtigs SSHash-Lite: https://github.com/jermp/sshash-lite

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Schmidt, S., Khan, S., Alanko, J., Tomescu, A. I.. 2021-12-17. Matchtigs: minimum plain text representation of kmer sets. https://doi.org/10.1101/2021.12.15.472871

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