Extremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT

Abstract

AbstractCompacted de Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted graphs Bruijn graphs are a variant built on acollectionof sequences, and associate to eachk-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based on a new approach merging thek-mer counting step with the unitig construction step, and on numerous practical optimizations.For compacted de Bruijn graph construction, GGCAT achieves speed-ups of 3–21× compared to the state-of-the-art tool Cuttlefish 2 (Khan and Patro, Genome Biology, 2022). When constructing the colored variant, GGCAT achieves speed-ups of 5–39× compared to the state-of-the-art tool BiFrost (Holley and Melsted, Genome Biology, 2020). Additionally, GGCAT is up to 480× faster than BiFrost for batch sequence queries on colored graphs.