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


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.




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