hmm I don`t think so I fathom the complete complexity of the process but with so many powerful GPU`s out there, is there a possibility of reconstruction in a matter of days if not hours?
If you are further interested in parallelization schemes for genomic pipelines, please have a look at our paper on the strengths and limitations of big data technology for genomic analysis (published last week) - https://people.cs.umass.edu/~aroy/sigmod17-roy.pdf
In addition to our company, Genomenon (which seeks to speed up the interpretation time required to analyze the data _after_ it's been computationally aligned and annotated), I'm also friends with another startup down the street, called Parabricks, which seeks to speed up this alignment process (aka secondary analysis) even further.