De novo genome assembly of next-generation sequencing data is a fundamental problem in bioinformatics. There are many programs that assemble small genomes, but very few can assemble whole human genomes. We present a new algorithm for parallel overlap graph construction, which is capable of assembling human genomes and improves upon the current state-of-the-art in genome assembly.

Availability and implementation

SAGE2 is written in C ++ and OpenMP and is freely available (under the GPL 3.0 license) at

Supplementary information

Supplementary data are available at Bioinformatics online.

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