License: Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.CPM.2019.7
URN: urn:nbn:de:0030-drops-104782
URL: https://drops.dagstuhl.de/opus/volltexte/2019/10478/
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Prezza, Nicola ; Rosone, Giovanna

Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform

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LIPIcs-CPM-2019-7.pdf (0.6 MB)


Abstract

We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1,sigma] can be computed from the Burrows-Wheeler transformed collection in O(n log sigma) time using o(n log sigma) bits of working space on top of the input and output. Our result improves (on small alphabets) and generalizes (to string collections) the previous solution from Beller et al., which required O(n) bits of extra working space. We also show how to merge the BWTs of two collections of total size n within the same time and space bounds. The procedure at the core of our algorithms can be used to enumerate suffix tree intervals in succinct space from the BWT, which is of independent interest. An engineered implementation of our first algorithm on DNA alphabet induces the LCP of a large (16 GiB) collection of short (100 bases) reads at a rate of 2.92 megabases per second using in total 1.5 Bytes per base in RAM. Our second algorithm merges the BWTs of two short-reads collections of 8 GiB each at a rate of 1.7 megabases per second and uses 0.625 Bytes per base in RAM. An extension of this algorithm that computes also the LCP array of the merged collection processes the data at a rate of 1.48 megabases per second and uses 1.625 Bytes per base in RAM.

BibTeX - Entry

@InProceedings{prezza_et_al:LIPIcs:2019:10478,
  author =	{Nicola Prezza and Giovanna Rosone},
  title =	{{Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform}},
  booktitle =	{30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)},
  pages =	{7:1--7:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-103-0},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{128},
  editor =	{Nadia Pisanti and Solon P. Pissis},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2019/10478},
  URN =		{urn:nbn:de:0030-drops-104782},
  doi =		{10.4230/LIPIcs.CPM.2019.7},
  annote =	{Keywords: Burrows-Wheeler Transform, LCP array, DNA reads}
}

Keywords: Burrows-Wheeler Transform, LCP array, DNA reads
Collection: 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Issue Date: 2019
Date of publication: 06.06.2019


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