CSTs for Terabyte-Sized Data

Generating pangenomic datasets is becoming increasingly common but there are still few tools able to handle them and even fewer accessible to non-specialists. Building compressed suffix trees (CSTs) for pangenomic datasets is still a major challenge but could be enormously beneficial to the community. In this paper, we present a method, which we refer to as RePFP-CST, for building CSTs in a manner that is scalable. To accomplish this, we show how to build a CST directly from VCF files without decompressing them, and to prune from the prefix-free parse (PFP) phrase boundaries whose removal reduces the total size of the dictionary and the parse. We show that these improvements reduce the time and space required for the construction of the CST, and the memory footprint of the finished CST, enabling us to build a CST for a terabyte of DNA for the first time in the literature.