  Motivation: De Bruijn graphs have been proposed as a data structure to
facilitate the analysis of related whole genome sequences, in both a population
and comparative genomic settings. However, current approaches do not scale well
to many genomes of large size (such as mammalian genomes). Results: In this
paper, we present TwoPaCo, a simple and scalable low memory algorithm for the
direct construction of the compacted de Bruijn graph from a set of complete
genomes. We demonstrate that it can construct the graph for 100 simulated human
genomes in less then a day and eight real primates in less than two hours, on a
typical shared-memory machine. We believe that this progress will enable novel
biological analyses of hundreds of mammalian-sized genomes. Availability: Our
code and data is available for download from github.com/medvedevgroup/TwoPaCo
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