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Comment by hxrts | Hacker News Reader

One point worth mentioning. Ion Torrent is one of several companies that develops high-throughput or 'nextgen' sequencing platforms 454 and Illumina being the other big players right now. Each technology has a few important nuances that make them better or worse for a particular project. Some of the major things one looks at are cost of the device and library construction, error rates due to PCR amplification steps or nucleotide calling, library sizes, and maximum read length but there are many more. In addition, pore technologies will definitely become important in the near future because they enable single molecule experiments which are currently impossible without amplification using the above platforms.

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Ion torrent appears to be the same platform as 454, but with detection via chemical means (ISFETs) rather than optical transduction. One of the big drawbacks of the 454 technology that doesn't get talked about a lot is that the immulsion PCR/microbeads require a lot of preparation before the actual sequencing run. On the 454, I believe the sequencing time was ~8hrs, but the preparation time (at least at the facility where I was involved) typically took more than 8 hrs. In terms of actual sequencing time, it's the best system. But as you said, read length is a major issue with all of the current "nextgen" systems that should be resolved with nanopore sequencing.

From a clinical / experimental standpoint there's very little difference between 4,8,16 hours. It's all essentially 'next day' right now because common practice is to send the sample off to a genomics core and they drop the data on a server for you after they've run it through their pipeline. Many experiments require their own library construction but clinical pipelines generally don't and again, the machine prep time is not the bottleneck it's deciding what to include and how to lay things out. From what I understand 454 accommodates the longest read lengths right now but this seems to change month to month, also from what I understand 454 has a lot of trouble with short length libraries.

PacBio has average read length now of about 5000 bp whereas 454 is still only about 1000 bp.

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