The Helicos stuff would have to be pretty old, they've been effectively out of business for some time (having filed for bankruptcy in 2012).
The paper suggests they mostly used Illumina, with one guy using Helicos:
"J.S. did ancient and modern DNA extractions and constructed Illumina DNA libraries for shotgun sequencing"..."X.W. did Illumina libraries on donkey extracts"..."A.S.-O. performed Illumina sequencing for the Middle Pleistocene".."Ji.M. and X.W. performed Illumina sequencing for the Middle Pleistocene and the donkey genomes at BGI".."J.F.T. headed true Single DNA Molecule Sequencing of the Middle Pleistocene genome"
It's worth noting that while Illumina sequencing isn't true single molecule, you are getting a read signal from a single fragment of DNA.
“But also we pioneered the usage of what is called true Single Molecular Sequencing that basically reads through molecules as they stand, without further manipulation,” Orlando added. By tracking a full, single DNA molecule, the team was able to avoid having to “amplify” fragments, which can often introduce errors.
This is utterly silly because the technique they used (illumina) amplifies fragments anyways, and the error introduced by PCR (1 in 40,000 if you use good polymerases) would pale in comparison to the molecular degradation; it should be simple to run control experiments and "back out" the amount of error caused by the manipulation.
It's also worth noting that this is not a full genome, they just sequenced PARTS of the genome.
