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Based on what's known today, what factors would enter into selecting the new PacBio analyzer versus, say, the HiSeq2000 for either whole genome or exome resequencing?
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From the specs I've seen, PacBio will not initially be cost-effective vs. HiSeq in those domains.
Strengths for PacBio are very rapid turnaround, relatively simple sample prep, low cost per run (really "shot") and very long read lengths. In my mind, whole genome sequencing doesn't leverage any of those & quick back-of-envelope calculations put a PacBio human genome at many times an Illumina or SOLiD one. -
In short, my opinion one wouldn't choose one over the other. The PacBio, in my opinion, fills a different niche than the HiSeq2000/SOLiD4/etc. Therefore, optimally you would have multiple platforms for their specific purposes. In PacBio's case, scaffolding and potentially base kinetics come to mind as things it does that the other major platforms don't.Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]Comment
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