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Newbie question: For few years I have seen news like “Whole-genome sequencing” is now under $1000 etc. I believed that this means all the base pairs of all chromatids in a single cell are identified and stored in a digital format in the original sequence. Just checked this Wikipedia article as well, which seem to align with my understanding.

Today I saw many news articles saying that Y-chromosome was fully sequenced for the first time. For example this article, which also mention that other chromosomes were fully sequenced only early this year.

What am I missing? Perhaps "Whole" is not "whole"?

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So in short, the human genome project (HGP) and Greg Venter with his companies (fascinating story, I recommend to read into it) were unable to sequence many heterochromatic regions (with lots of repeats). Why? Because for repeats you need long-read sequencing methods (e.g., Nanopore, PacBio) that only became available in recent years. So apparently the HGP and subsequent attempts left out about 8% of the genome (https://www.science.org/doi/10.1126/science.abj6987), which simply consisted of some repeats and as the believe at that time was anyway that all these repeats are "junk" and the genes (about 2-3% of the genome) are the important stuff, they could argue that they sequenced the "whole" genome. Now of course we know that also repeats can be important for disease, gene novelty (evolution) etc. Hope that helps.

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