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

Compacted de Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a of sequences and associate to each -mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based on a new approach merging the -mer counting step with the unitig construction step, as well as on numerous practical optimizations.