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Pacific Biosciences of California, Inc. Message Board

  • codyoot codyoot May 17, 2013 10:52 AM Flag

    an expert's take on genome assembly

    Dr. Keith Robison, Principal Scientist at Warp Drive Bio fas blogged the following: I'm going to attempt to say there's not one right approach to sequencing a genome, though for small genomes (

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    • though for small genomes (

      • 1 Reply to codyoot
      • I'm going to attempt to say there's not one right approach to sequencing a genome, though for small genomes I'm starting to think there is pretty much one way: Pacific Biosciences long libraries at 100+X coverage. As shown in a recent pre-print, this strategy will assemble most bacterial genomes into a very small number of contigs, perhaps one per replicon. In my own hands, it isn't quite that good on difficult genoems, but it is the best out there. If you are sequencing only a single small genome, Pacific Biosciences may even be cost competitive with a single MiSeq run. Clearly here I'm talking renting not buying; but there's a lot of free capacity you can rent at a modest price. At this moment in time (May 2012), a bacterial genome can be sequenced for about $1K plus perhaps $100 of processing if you do it at Amazon (as noted by a commenter on a previous post, other platforms spit out ready-to-go data but PacBio requires a bunch of processing; don't let that scare you off!).

 
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