The hg38 genome, and earlier published human genomes, contained regions of DNA that were very difficult or impossible to sequence using short read "Next Generation" sequencers.? In short reads only the first 150 or so nucleotides are sequenced at either end of the DNA fragments.? I understand that the sequencing difficulty was caused by those parts of the human genome that are very repetitious.? The T2T reference genome, which was released in March 2022, used more recent "long read" sequencing technology to determine the nucleotide sequence for all regions of the genome, filling in all of the unsequenced gaps that existed in the hg38 genome.? Long read sequencers are able to recover sequences containing many thousands of nucleotides, but usually with a higher density of sequencing errors.
Will there be any great benefit to genetic genealogists to use realign their short read datasets against the gapless T2T genome?? I suspect that there would be relatively little benefit since the gaps that that are now covered in T2T probably didn't contain much useful information for genetic genealogy purposes.? But perhaps the T2T made corrections to other genealogically significant parts of the genome, sections that were not correctly sequenced in hg38, such as in the notoriously repetitious Y chromosome.? The upgrade cost of
€23 is modest, and so I would encourage you to give it a try and then report on any interesting changes that you obtained.
