A large (and small) de novo genome assembler. DISCOVAR de novo quickly generates highly accurate and complete assemblies using the same single library data. It requires reads from only a single PCR-free library, and has tested well on relatively homozygous human and mouse genomes. DISCOVAR de novo has the potential to create, from relatively inexpensive sequencing libraries and read coverage, assemblies that are sufficiently complete and contiguous to serve a wide range of downstream comparative, population, and functional genomic analyses.