Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT [METHOD]

We present GGCAT, a tool for constructing both types of graphs, based on a new approach merging the k-mer counting step with the unitig construction step, as well as on numerous practical optimizations. For compacted de Bruijn graph construction, GGCAT achieves speed-ups of 3x to 21x compared with the state-of-the-art tool Cuttlefish 2. When constructing the colored variant, GGCAT achieves speed-ups of 5x to 39x compared with the state-of-the-art tool BiFrost. Additionally, GGCAT is up to 480x faster than BiFrost for batch sequence queries on colored graphs.

Source: Genome Research - August 9, 2023 Category: Genetics & Stem Cells Authors: Cracco, A., Tomescu, A. I. Tags: METHOD Source Type: research