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 collection of sequences and associate to each k-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 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 3× to 21× compared with the state-of-the-art tool Cuttlefish 2. When constructing the colored variant, GGCAT achieves speed-ups of 5× to 39× compared with the state-of-the-art tool BiFrost. Additionally, GGCAT is up to 480× faster than BiFrost for batch sequence queries on colored graphs.

中文翻译：

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使用 GGCAT 极其快速地构建和查询压缩和彩色 de Bruijn 图

压缩 de Bruijn 图是计算基因组学中最基本的数据结构之一。彩色压缩 de Bruijn 图是建立在序列集合上的变体，并将每个k聚体与其出现的序列相关联。我们提出了 GGCAT，一种用于构建两种类型图的工具，基于将k聚体计数步骤与 unitig 构建步骤合并的新方法以及大量实际优化。对于紧凑的 de Bruijn 图构建，与最先进的工具 Cuttlefish 2 相比，GGCAT 实现了 3 倍到 21 倍的加速。在构建彩色变体时，GGCAT 与最先进的工具 Cuttlefish 2 相比，实现了 5 倍到 39 倍的加速使用最先进的工具 BiFrost。此外，对于彩色图上的批量序列查询，GGCAT 比 BiFrost 快 480 倍。