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International Symposium on String Processing and Information Retrieval

SPIRE 2019: String Processing and Information Retrieval pp 304–321Cite as

An Index for Sequencing Reads Based on the Colored de Bruijn Graph

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11811))

Abstract

In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a color matrix C. To reduce the space requirements, we devise an algorithm that produces a smaller and more sparse version of C. The novelties in this algorithm are (i) an incomplete coloring of the graph and (ii) a greedy coloring approach that tries to reuse the same colors for different strings when possible. We also propose two algorithms that work on top of the index; one is for reconstructing reads, and the other is for contig assembly. Experimental results show that our data structure uses about half the space of the plain representation of the set (1 Byte per DNA symbol) and that more than 99% of the reads can be reconstructed just from the index.

Partially supported by Basal Funds FB0001, Conicyt, Chile; by a Conicyt Ph.D. Scholarship; by Fondecyt Grants 1-171058 and 1-170048, Chile; and by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie [grant agreement No. 690941].

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Notes

  1. 1.

    http://spades.bioinf.spbau.ru/spades_test_datasets/ecoli_mc.

  2. 2.

    https://bitbucket.org/DiegoDiazDominguez/colored_bos/src/master.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Chile, Santiago, Chile

    Diego Díaz-Domínguez

  2. CeBiB — Center for Biotechnology and Bioengineering, University of Chile, Santiago, Chile

    Diego Díaz-Domínguez

Authors
  1. Diego Díaz-Domínguez
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Correspondence to Diego Díaz-Domínguez .

Editor information

Editors and Affiliations

  1. University of A Coruña, A Coruña, Spain

    Nieves R. Brisaboa

  2. University of Helsinki, Helsinki, Finland

    Simon J. Puglisi

A Appendix

A Appendix

1.1 A.1 Pseudocodes

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Díaz-Domínguez, D. (2019). An Index for Sequencing Reads Based on the Colored de Bruijn Graph. In: Brisaboa, N., Puglisi, S. (eds) String Processing and Information Retrieval. SPIRE 2019. Lecture Notes in Computer Science(), vol 11811. Springer, Cham. https://doi.org/10.1007/978-3-030-32686-9_22

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  • DOI: https://doi.org/10.1007/978-3-030-32686-9_22

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-32685-2

  • Online ISBN: 978-3-030-32686-9

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