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arXiv · 2506.03294

Prefix-free parsing for merging big BWTs

Diego Diaz-Dominguez·Travis Gagie·Veronica Guerrini·Ben Langmead·Zsuzsanna Liptak·Giovanni Manzini·Francesco Masillo·Vikram Shivakumar
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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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Diego Diaz-Dominguez, Travis Gagie, Veronica Guerrini, Ben Langmead, Zsuzsanna Liptak, Giovanni Manzini, Francesco Masillo, Vikram Shivakumar. 2025-06-03. Prefix-free parsing for merging big BWTs. https://arxiv.org/abs/2506.03294

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