Compression Algorithm for Colored de Bruijn Graphs

Authors Amatur Rahman , Yoann Dufresne, Paul Medvedev

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Amatur Rahman
  • Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA
Yoann Dufresne
  • Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, Paris, France
  • Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
Paul Medvedev
  • Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA
  • Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
  • Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA


We would like to thank R. Chikhi for helpful discussions.

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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)


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.

Subject Classification

ACM Subject Classification
  • Applied computing → Computational biology
  • colored de Bruijn graphs
  • disk compression
  • k-mer sets
  • simplitigs
  • spectrum-preserving string sets


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