ALLPATHS-LG (Large Genome) is a whole genome shotgun assembler that can generate high quality assemblies from short reads. It works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.
Computational R&D, The Broad Institute, Cambridge, MA
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Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2010.
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proceedings of the National Academy of Sciences USA (epub ahead of print, Dec. 27, 2010).