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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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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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