Prefix-free parsing for merging big BWTs

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Authors Diego Diaz-Dominguez, Travis Gagie, Veronica Guerrini, Ben Langmead, Zsuzsanna Liptak, Giovanni Manzini, Francesco Masillo, Vikram Shivakumar arXiv ID 2506.03294 Category cs.DS: Data Structures & Algorithms Citations 2 Venue SPIRE Last Checked 4 months ago
Abstract
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very similar to each other -- such as collections of many copies of genomes of each of several species, or collections of many copies of each of the human chromosomes -- then we can drastically reduce PFP's memory footprint by building the BWTs of the small datasets and then merging them into the BWT of the whole dataset.
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