Description
This set of tracks provides per base alignment for all T2T primate assemblies by the Telomere-to-Telomere consortium and the draft human pangenome reference assemblies by the Human Pangenome Reference Consortium.
Methods
- We applied WFMASH to align all assemblies against all T2T primate assemblies using each one as reference (target). We filtered out alignments shorter than 25kbp and with identity lower than ~70%.
wfmash -t 48 -P "$TARGET#" --one-to-one -Y "#" -n 1 -p 70 -s 5k -c 20k primates16.20231205.fa.gz > $TARGET.p70.aln.paf
-
We used PAF2CHAIN to convert aligned PAF files to CHAIN files.
paf2chain -i $TARGET.p70.aln.paf -o $TARGET.p70.aln.chain
For a full description of the methods, refer to the ape_pangenome repository.
Credits
Track supplied by Andrea Guarracino and Erik Garrison in the University of Tennessee Health Science Center.
References