A group of scientists is reporting that they have the first gapless telomere to telomere sequence for a human chromosome. They used nanopore sequencing which allows really long sequencing reads that overcome the problems caused by assembling many short reads. You can check out the paper here:
So these gaps that we currently have are just hard to sequence? Do we know what percentage of the total genome are gaps?
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Some are hard to sequence, but most are just hard to assemble. Lots of short repeats. There’s an estimate of the percentage of gaps in the cited article.
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Ah, so if you’re doing bit-by-bit then it’s hard to tell how many repeats might be in a given long stretch?
OK, I looked real quick but must have missed it.
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Yes, and it’s hard to tell where a bit is in a long stretch of repeats or know where that bit is in relation to other, similar bits. Consider these two fragments: ATATATATATATAT and TATATATATATATAT. How would you fit them together, particularly considering that the full sequence might have hundreds of AT repeats? (This is an artificial example: repeats and sequenced fragments are much longer than that. But you get the idea.)
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Larry Moran has a good blog post on this.
Moran’s blog is also where I learned about the complete sequencing of the X chromosome.
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