4 ms·

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 ma

• JangoSteve 10y ago
  Yes, it depends on the size of the sequencing panel that was done (i.e. a targeted panel for a specific gene or set of genes versus whole exome versus whole genome). But even for whole exome, you're talking a few hours or faster depending on hardware. 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.
• virtuabhi 10y ago
  The steps in the genomic analysis pipelines are not always embarrassingly parallel. The degree of parallelization cannot be increased to an arbitary number. In addition, the parallel executions can give slightly different results when compared with the serial output, so we need "safe" data-partitioning schemes and rigorous error control. 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 https://people.cs.umass.edu/~aroy/sigmod17-roy.pdf