Work

Compression algorithm for colored de Bruijn graphs

Year: 2024

Type: article

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. The software is available at http://github.com/medvedevgroup/ESSColor .

Source: Algorithms for Molecular Biology

DOI: 10.1186/s13015-024-00254-6

Authors: Amatur Rahman, Yoann Dufresne, Paul Medvedev

Institutions: Pennsylvania State University, Institut Pasteur, Université Paris Cité

Language: English

Topic: Algorithms and Data Compression

Subfield: Artificial Intelligence

Field: Computer Science

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $2,390