Talk:Ion semiconductor sequencing

Lead
Says ion semiconductor sequencing is AKA "pH-mediated sequencing" - this is misleading at best, inaccurate at worst. I've never heard it called that (minor, possibly insignificant point). Nothing about the sequencing is "mediated" by pH. It is true that the method detects protons produced by nucleotide incorporation, but protons do not mediate sequencing any more than any other method. MRotten (talk) 15:09, 28 August 2019 (UTC)

Comment
Hi, in the table "Comparison to other sequencing methods" you compare apples and oranges, both 454 and Illumina launched bench top sequencing platforms last year. They have both similar, output, cost per run and instrument costs. — Preceding unsigned comment added by 178.190.89.38 (talk • contribs) 21:15, 5 July 2012 (UTC)

The article mentions "throughput" in the "Limitations" section, and I would like to inform editors that this isn't such a great term. As I understand it, this is a qualitative metric (dare I say it's a marketing term?) that is used to describe how much information you can get from the system in a given time. However, the information part of that definition is not clearly defined. It is clear that a higher 'throughput' system is one with individual long read lengths, or more reads per run, or shorter run times. In other words, a system is said to be high-throughput if each run contains more information than some other system, or if each run gives more reads than some other system, or if the run time is shorter than some other system. Throughput also varies by experiment. For example, if you're doing SNP detection, you'd want info from a lot of variants, but you don't need a lot of info from each one, so the higher throughput system is one which produces the highest number of reads, regardless of read length. In this case, Illumina Solexa (relatively short read lengths) might be said to be higher throughput than the PacBio RSII (long read lengths). For de-novo genome assembly, in which both ends of each read has to overlap with some other read to allow a contig to be assembled, the RSII would be the higher throughput platform because redundant information would comprise a smaller fraction of each read (in theory). I propose the "Limitations" section first talk about average read length (which it does), then average reads per run, then average run time, and that any discussion of throughput be either omitted or defined in context. MRotten (talk) 17:51, 16 November 2015 (UTC)

Strengths/Limitations
So far, what I know, pyrosequencing provides about same read lenght as IonTorrent, sangers allows longer reads, but it is not used for genome assembly at all. Long reads platforms MinION and Sequel provide reads of lenght of thousands kbs, another plotform widely used for assembly is HiSeq using pair end reads. -Kamil — Preceding unsigned comment added by 82.152.153.29 (talk) 22:30, 17 December 2015 (UTC)
 * Agree with this comment. Additionally, 454 pyrosequencing is a dead technology, in that this is no longer commercially available. Qiagen has a non-MPS pyrosequencing platform, but it is not comparable to modern ion semiconductor sequencing systems. MRotten (talk) 16:13, 28 August 2019 (UTC)

The references for "rapid sequencing speed and low upfront and operating costs" are two articles, one published in 2008 (11 years ago as of this writing) and the other published in 2011 (9 years ago as of this writing). All still-available MPS technologies have made significant advancements since then, so many forward-looking statements and comparisons to other technologies are no longer relevant. Instead of discussing strengths/limitations in terms of competitors, I would propose that the discussion of strengths/limitations 1) be limited to the performance of the systems at the time of the writing and 2) make no comparisons to other systems whose limitations and strengths will likely also change in the near future, or might not be available. MRotten (talk) 15:28, 28 August 2019 (UTC)

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