The Denisova Genome Consortium have released for public use the raw sequence data, alignments and genotype calls for the high-coverage genome sequence of a Denisovan individual, as well as the modern human sequences presented in the publication.
When using this genome data please cite the following publication:
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D, Kelso J, Paabo S: A High-Coverage Genome Sequence from an Archaic Denisovan Individual.Science. Aug 31 2012.
Provided here are the alignments using BWA to the human (hg19/GRCh37) and chimpanzee (panTro2) genomes.