An algorithm for whole genome assembly of deep paired-end short reads. Meraculous relies on an efficient and conservative traversal of a subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset. Unlike other short-read assemblers, Meraculous avoids an explicit error correction step, instead relying on base quality scores. Meraculous also incorporates a novel low-memory hash structure to access the deBruijn graph, allowing a small memory footprint compared with other short-read assemblers.