Pangenome Optimization via Elastic Degenerate Strings

Abstract: An Elastic Degenerate String (EDS, or ED-string) is a sequence of string sets. A pangenome, consisting of variations observed in a population along the genome sequences, can be naturally encoded as an EDS. Pattern matching and comparison problems on pangenome representations such as EDSes have been widely studied in the literature, but optimizing the pangenome properties during its construction has been largely omitted. We fill this gap by showing how methods originally developed for the related problem of founder reconstruction can be adapted to minimize, in linear time, the total cardinality of the EDS sets or the total size of the EDS strings, given suitable multiple alignments representing the input data. We provide an implementation for the minimum-cardinality criterion in a tool mincard, and conduct the first experiments on scalable pangenome optimization via EDSes. The code and experiments are available at https://github.com/algbio/eds.