The first draft of a human pangenome reference — a collection that aims to eventually represent as many as possible of the DNA sequences found across our species — is published in Nature today
The reliable and unreliable regions for all haplotype assemblies were aligned to T2T-CHM13 and then subdivided into 5 kb windows and intersected with the SD annotations for T2T-CHM13. SD annotations were unavailable for chromosome Y on T2T-CHM13 at the time of analysis. Furthermore, the chromosome Y added to T2T-CHM13 is from the HPRC HG002 sample; therefore chromosome Y was excluded.
The sequence-selected region or regions were then retrieved and aligned against the corresponding GRCh38 region using MAFFT. For each gene, the corresponding exons were retrieved and the coordinates were projected through the alignment of the two regions. Transcripts were then reconstructed from the projected exons. For each transcript, the coverage and identity when aligned to the parent transcript from GRCh38 were calculated.
To minimize the occurrences of mis-mapped paralogues, each gene was checked for exon overlap in both the target and the reference. If the overlapping genes were not identical at a locus between the reference and the target, then a conflict was identified.
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