Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k -mer of the graph to the genomes it occurs in. Availability https://github.com/pmelsted/bifrost

中文翻译：

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Bifrost：彩色和压缩 de Bruijn 图的高度并行构造和索引

de Bruijn 图的内存消耗通常令人望而却步。大多数基于 de Bruijn 图的汇编程序通过将路径压缩为单个顶点来降低复杂性，但这具有挑战性，因为它需要未压缩的 de Bruijn 图在内存中可用。我们提出了一种并行且内存高效的算法，可以直接构建压缩的 de Bruijn 图，而无需生成中间的未压缩图。Bifrost 具有广泛的功能，例如索引、编辑和查询图形，并包括一种图形着色方法，可将图形的每个 k 聚体映射到其所在的基因组。可用性 https://github.com/ pmelsted/bifrost