Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. SOAPdenovo is made up of six modules that handle read error correction, de Bruijn graph (DBG) construction, contig assembly, paired-end (PE) reads mapping, scaffold construction, and gap closure. The major last improvements of SOAPdenovo are: i) enhancing the error correction algorithm, ii) providing a reduction in memory consumption in DBG constructions, iii) resolving longer repeat regions in contig assembly, iv) increasing assembly length and coverage in scaffolding and v) improving gap closure.