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DOI: 10.4230/LIPIcs.WABI.2023.17

Compression Algorithm for Colored de Bruijn Graphs

Authors: Amatur Rahman, Yoann Dufresne, and Paul Medvedev

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract

A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead.

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Amatur Rahman, Yoann Dufresne, and Paul Medvedev. Compression Algorithm for Colored de Bruijn Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 17:1-17:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{rahman_et_al:LIPIcs.WABI.2023.17,
  author =	{Rahman, Amatur and Dufresne, Yoann and Medvedev, Paul},
  title =	{{Compression Algorithm for Colored de Bruijn Graphs}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{17:1--17:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.17},
  URN =		{urn:nbn:de:0030-drops-186434},
  doi =		{10.4230/LIPIcs.WABI.2023.17},
  annote =	{Keywords: colored de Bruijn graphs, disk compression, k-mer sets, simplitigs, spectrum-preserving string sets}
}

Document

DOI: 10.4230/LIPIcs.WABI.2020.11

A Graph-Theoretic Barcode Ordering Model for Linked-Reads

Authors: Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, and Rayan Chikhi

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract

Considering a set of intervals on the real line, an interval graph records these intervals as nodes and their intersections as edges. Identifying (i.e. merging) pairs of nodes in an interval graph results in a multiple-interval graph. Given only the nodes and the edges of the multiple-interval graph without knowing the underlying intervals, we are interested in the following questions. Can one determine how many intervals correspond to each node? Can one compute a walk over the multiple-interval graph nodes that reflects the ordering of the original intervals? These questions are closely related to linked-read DNA sequencing, where barcodes are assigned to long molecules whose intersection graph forms an interval graph. Each barcode may correspond to multiple molecules, which complicates downstream analysis, and corresponds to the identification of nodes of the corresponding interval graph. Resolving the above graph-theoretic problems would facilitate analyses of linked-reads sequencing data, through enabling the conceptual separation of barcodes into molecules and providing, through the molecules order, a skeleton for accurately assembling the genome. Here, we propose a framework that takes as input an arbitrary intersection graph (such as an overlap graph of barcodes) and constructs a heuristic approximation of the ordering of the original intervals.

Cite as

Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, and Rayan Chikhi. A Graph-Theoretic Barcode Ordering Model for Linked-Reads. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 11:1-11:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{dufresne_et_al:LIPIcs.WABI.2020.11,
  author =	{Dufresne, Yoann and Sun, Chen and Marijon, Pierre and Lavenier, Dominique and Chauve, Cedric and Chikhi, Rayan},
  title =	{{A Graph-Theoretic Barcode Ordering Model for Linked-Reads}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{11:1--11:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.11},
  URN =		{urn:nbn:de:0030-drops-128001},
  doi =		{10.4230/LIPIcs.WABI.2020.11},
  annote =	{Keywords: DNA sequencing, graph algorithms, linked-reads, interval graphs, cliques}
}

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Documents authored by Dufresne, Yoann

Compression Algorithm for Colored de Bruijn Graphs

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A Graph-Theoretic Barcode Ordering Model for Linked-Reads

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