From their site:
The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).It then appears that Neandertals occupied the same cave as the elusive Denisovans. When? I guess we'll have to wait to find out, but the preliminary genetic analysis shown on the figure (top-left) makes it clear that the "Altai" specimen marked in red which is the source of the high-coverage Neandertal genome does indeed group with other Neandertals, while Denisova is more related to Neandertals than to modern humans.
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.
I've highlighted this before, but it bears repeating: divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart-- seems to exceed that found between any two modern human groups which span the entire Earth.