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In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the DNA sequencing:

In reality, most nuclear genomes are a mixture of unique sequences and short and long repeats of various kinds, and researchers have developed ways of dealing with the issue. One approach is to obtain sequences from both ends of the randomly selected DNA fragments (see Figure 6), and to have the algorithm keep track of these so-called ‘paired ends’ and the distance between them (which is known because the genomic DNA was size-selected prior to library construction and sequencing). This improves the chances of being able to anchor the sequence data from each DNA fragment onto the genome. It is also common to perform multiple sequencing runs using DNA that has been sheared to different sizes (e.g. 2, 10, and 50 Kbp); this makes paired-end data even more effective in overcoming the problems associated with repetitive DNA.

I don't have enough knowledge about this topic, and I'm not sure of the exact meaning of "run" in this context. Does it mean "performing the process of sequencing multiple times" or "generating multiple sequences"?

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    $\begingroup$ This is English not Biology. I suggest you abbreviate the question and transfer it to SE English Language Learners. $\endgroup$
    – David
    Aug 25, 2022 at 8:55
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    $\begingroup$ @david ‘run’ is a technical scientific term that’s used often, and asking about terminology is on topic here. Most importantly, this is likely to be useful to biologists, so I disagree with your suggestion. $\endgroup$
    – user438383
    Aug 25, 2022 at 11:27
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    $\begingroup$ @user438383 See Merriam-Webster Run noun "4 : a continuous period or series especially of things of identical or similar sort" with 7 examples, including ": a set of consecutive measurements, readings, or observations". The poster seems to be trying to use this site as a consultancy to help him reading a book, rather than asking questions about biology arising from it. I would encourage him to learn to save his own life. $\endgroup$
    – David
    Aug 25, 2022 at 15:51
  • $\begingroup$ It looks to me like that sentence should really read "It is common to prepare multiple sequencing libraries using DNA that has been sheared to different sizes". While you can run the same library over and over again, since one run is only a sampling of the library contents, it looks to me like the author is talking about combining information from libraries of different insert sizes as being more effective than resampling from one library with one target insert size. $\endgroup$
    – swbarnes2
    Aug 31, 2022 at 0:43

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Each run is simply each time a reaction/process is performed, though usually applied to something that is performed on a machine or device that does the "running" - so you could do quantitative PCR runs or run a gel.

Multiple runs would be repeated reactions/processes (in this case sequencing library preparation then run on the sequencing device).

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  • $\begingroup$ DNA sequencing (e.g. Illumina dye sequencing) does not sequence all DNA available; it simply sequences a sample of what you provide, i.e. it "samples". Say you have a bag of 100 differently-colored ping pong balls, and you have a set procedure wherein you take out 50 balls at random and note down their color to understand the color distribution. You could do this "run" once, but you can get a better, more reliable look into your bag if you do a 50-ball-random-sampling multiple times! You do many "runs". That's why in research we use the phrase "multiple runs" when we have preset procedures. $\endgroup$
    – S Pr
    Aug 25, 2022 at 10:11
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    $\begingroup$ ^above is addendum to answer to help make it more intuitive, i make no comment on the actual answer, it's very good. +1 $\endgroup$
    – S Pr
    Aug 25, 2022 at 10:13

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