What are the appropriate terms and defintions in sequencing?
It seems that there is no agreement on the usage of some terms in massively parallel sequencing. For example, the SAM specifications define as "segment" what many would call "read", namely "A contiguous (sub)sequence on a template which is sequenced or assembled." And I understand that their definition of "read" would include the two paired ends of a template sequenced by Illumina, e.g. So, according to SAM specifications, we could say "discordant read", instead of "discordant pair"; and it would not be appropriate to refer to a single end with the term "read". Convenient as it seems to standardize the use of these terms, the truth is that I don't see the terms used in the literature in the way suggested by SAM.
Another problematic term is "insert", when applied to the fragment of DNA between the two sequenced ends of a pair, which may have never been "inserted".
Then, the terms "clonal coverage", "span coverage", and also "physical coverage" have been used with apparently the same meaning.
Lastly, I'm bothered by the flashy qualifier of the "next generation" sequencing. Doesn't it make more sense to say something less ephemeral, like "massively parallel" sequencing?
I welcome any recommendation, reference, guidance or comment on the appropriate usage of these terms.
Another problematic term is "insert", when applied to the fragment of DNA between the two sequenced ends of a pair, which may have never been "inserted".
Then, the terms "clonal coverage", "span coverage", and also "physical coverage" have been used with apparently the same meaning.
Lastly, I'm bothered by the flashy qualifier of the "next generation" sequencing. Doesn't it make more sense to say something less ephemeral, like "massively parallel" sequencing?
I welcome any recommendation, reference, guidance or comment on the appropriate usage of these terms.
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