2013/02/28 by Kamil Salikhov, Salikhov, Kamil, Gustavo Sacomoto +3
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Advanced biosensing and bioanalysis techniques #Chromosomal and Genetic Variations #Data Structures and Algorithms (cs.DS) #E.2 #FOS: Computer and information sciences #Genomics and Phylogenetic Studies #J.3
paper · doi:10.48550/arxiv.1302.7278
openalex publication_date 2013/02/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs.