Description

These tracks show the regions unique to the T2T-CHM13 v2.0 assembly compared to the GRCh38/hg38 and GRCh37/hg19 reference assemblies.

Methods

Converting a chain file to the PAF format

We used the `to_paf.py` script from chaintools (https://doi.org/10.5281/zenodo.6342391, v0.1) to convert the v1_nfLO chains to the PAF format.

Obtaining unique regions

We used the follwing commands to obtain the regions unique to GRCh38/hg38 and GRCh37/hg19 in the BED format.

cut -f 1,3,4 grch38-chm13v2.paf  \
  | bedtools sort -i - -g chm13v2.0.fasta.fai \
  | bedtools merge \
  | bedtools complement -g chm13v2.0.fasta.fai -i - \
  | bedtools merge \
  > T2T-CHM13v2.0_unique_regions_hg38.bed

cut -f 1,3,4 hg19-chm13v2.paf |  bedtools sort -i - -g chm13v2.0.fasta.fai \
  | bedtools merge \
  | bedtools complement -g chm13v2.0.fasta.fai -i - \
  | bedtools merge \
  > T2T-CHM13v2.0_unique__regions_hg19.bed

Credits

The unique region annotations were generated by Nae-Chyun Chen<naechyun.chen@gmail.com> and Mitchell Vollger<mvollger@uw.edu>

References

Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. bioRxiv, 2021.