Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

Abstract

The de Bruijn graph has become a key data structure in modern computational genomics, and of keen interest is its compacted variant. The compacted de Bruijn graph provides a lossless representation of the graph, and it is often considerably more efficient to store and process than its non-compacted counterpart. Construction of the compacted de Bruijn graph resides upstream of many genomic analyses. As the quantity of sequencing data and the number of reference genomes on which to perform these analyses grow rapidly, efficient construction of the compacted graph becomes a computational bottleneck for these tasks.

We present Cuttlefish 2, significantly advancing the existing state-of-the-art methods for construction of this graph. On a typical shared-memory machine, it reduces the construction of the compacted de Bruijn graph for 661K bacterial genomes (2.58 Tbp of input reference genomes) from about 4.5 days to 17–23 hours. Similarly on sequencing data, it constructs the graph for a 1.52 Tbp white spruce read set in about 10 hours, while the closest competitor, which also uses considerably more memory, requires 54–58 hours.