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FWIW, the DNA was 100% sequenced. However, a proportion of that data that came back from the sequencing machine was too similar to each other, so it was impossi

FWIW, the DNA was 100% sequenced. However, a proportion of that data that came back from the sequencing machine was too similar to each other, so it was impossible to assemble it into a coherent full set of contiguous chromosomes. Imagine it like putting together a jigsaw puzzle, except that the picture on the front of the puzzle has lots of repeating motifs, so you end up with multiple pieces that look identical. You won't be able to tell how the whole thing fits together, but you can assemble the bits that are well-behaved and unique. Modern technology gives us larger jigsaw pieces, which allows us to distinguish between almost-identical parts of the puzzle better. But I would note that the project linked did a huge amount of sequencing using very expensive methods to be able to resolve the whole thing.

nzach 3y ago
For anyone interested, the problem mostly boils down to the sequence lenght we can read. Modern sequencing techniques allow us o read 200 to 500 bases at a time. So after hat we need do find a way o arrange these short sequences into a single sequence. And this can be prety hard, especially when you are doing 'de novo' assembly[0]. Besides that, there is the fact that some regions of DNA are repeated[1]. [0] - https://en.wikipedia.org/wiki/Third-generation_sequencing#De_novo_assembly https://en.wikipedia.org/wiki/Third-generation_sequencing#De... [1] - https://en.wikipedia.org/wiki/Repeated_sequence_(DNA) https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)
- gww 3y ago
  You are a bit behind on the available read lengths. The Oxford nanopore can produce reads as long as 300kb (k as in kilo) and the PacBio hifi can product 15 to 20kb reads. Finally a now defunct technology by 10x genomics called linked read sequencing also permitted longer regions to be sequences using short reads.
  - nzach 3y ago
    Thanks for pointing that out. My knowledge cut-off period in this domain is around 2018. So it's not suprising that things moved on.
nullfield 3y ago
So if one orders WGS at 30x or 100x from someplace like Nebula, what do you actually get?
- mnw21cam 3y ago
  Unless they're explicitly saying that you'll be getting long read sequencing, what you'll be getting is a paired-end short read sequencing, likely Illumina (although similar output can be achieved using BGI and Element machines as well). You'll be getting fragments of DNA which have been size-selected to around 400-500bp in length and then sequenced 150bp from both ends, with an unsequenced gap of unknown length in the middle (and possibly an overlap if the fragment is smaller than 300bp), sufficient to cover the mappable parts of the reference genome with around 30 or 100 sequence reads on average. That data can be supplied in a couple of FASTQ files (usually gzipped). They may offer to align that against a reference genome for you, where you'll get a BAM file - make sure you have the same reference genome handy to compare against. They may also offer to detect variants, that is places in the sequenced DNA that are different to the reference, in which case you'll get a VCF file. Because the sequencing uses short reads, it will not be able to resolve parts of the genome that are repetitive with a repeat unit longer than ~150bp. You'll have all the jigsaw pieces from the puzzle, but you won't be able to reconstruct some parts of the picture. Long read sequencing can help with those, but that's more expensive.

nzach 3y ago

For anyone interested, the problem mostly boils down to the sequence lenght we can read. Modern sequencing techniques allow us o read 200 to 500 bases at a time. So after hat we need do find a way o arrange these short sequences into a single sequence. And this can be prety hard, especially when you are doing 'de novo' assembly[0]. Besides that, there is the fact that some regions of DNA are repeated[1]. [0] - https://en.wikipedia.org/wiki/Third-generation_sequencing#De_novo_assembly https://en.wikipedia.org/wiki/Third-generation_sequencing#De... [1] - https://en.wikipedia.org/wiki/Repeated_sequence_(DNA) https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)

gww 3y ago
You are a bit behind on the available read lengths. The Oxford nanopore can produce reads as long as 300kb (k as in kilo) and the PacBio hifi can product 15 to 20kb reads. Finally a now defunct technology by 10x genomics called linked read sequencing also permitted longer regions to be sequences using short reads.
- nzach 3y ago
  Thanks for pointing that out. My knowledge cut-off period in this domain is around 2018. So it's not suprising that things moved on.

nullfield 3y ago

So if one orders WGS at 30x or 100x from someplace like Nebula, what do you actually get?

mnw21cam 3y ago
Unless they're explicitly saying that you'll be getting long read sequencing, what you'll be getting is a paired-end short read sequencing, likely Illumina (although similar output can be achieved using BGI and Element machines as well). You'll be getting fragments of DNA which have been size-selected to around 400-500bp in length and then sequenced 150bp from both ends, with an unsequenced gap of unknown length in the middle (and possibly an overlap if the fragment is smaller than 300bp), sufficient to cover the mappable parts of the reference genome with around 30 or 100 sequence reads on average. That data can be supplied in a couple of FASTQ files (usually gzipped). They may offer to align that against a reference genome for you, where you'll get a BAM file - make sure you have the same reference genome handy to compare against. They may also offer to detect variants, that is places in the sequenced DNA that are different to the reference, in which case you'll get a VCF file. Because the sequencing uses short reads, it will not be able to resolve parts of the genome that are repetitive with a repeat unit longer than ~150bp. You'll have all the jigsaw pieces from the puzzle, but you won't be able to reconstruct some parts of the picture. Long read sequencing can help with those, but that's more expensive.