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DOI: 10.4230/LIPIcs.WABI.2018.10

External memory BWT and LCP computation for sequence collections with applications

Authors: Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract

We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting the input collection into subcollections sufficiently small that it can compute their BWT in RAM using an optimal linear time algorithm. Next, it merges the partial BWTs in external memory and in the process it also computes the LCP values. We show that our algorithm performs O(n maxlcp) sequential I/Os, where n is the total length of the collection and maxlcp is the maximum LCP value. The experimental results show that our algorithm outperforms the current best algorithm for collections of sequences with different lengths and when the average LCP of the collection is relatively small compared to the length of the sequences. In the second part of the paper, we show that our algorithm can be modified to output two additional arrays that, combined with the BWT and LCP arrays, provide simple, scan based, external memory algorithms for three well known problems in bioinformatics: the computation of the all pairs suffix-prefix overlaps, the computation of maximal repeats, and the construction of succinct de Bruijn graphs.

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Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{egidi_et_al:LIPIcs.WABI.2018.10,
  author =	{Egidi, Lavinia and Louza, Felipe A. and Manzini, Giovanni and Telles, Guilherme P.},
  title =	{{External memory BWT and LCP computation for sequence collections with applications}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.10},
  URN =		{urn:nbn:de:0030-drops-93122},
  doi =		{10.4230/LIPIcs.WABI.2018.10},
  annote =	{Keywords: Burrows-Wheeler Transform, Longest Common Prefix Array, All pairs suffix-prefix overlaps, Succinct de Bruijn graph, Maximal repeats}
}

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External memory BWT and LCP computation for sequence collections with applications

Abstract

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