February 2024 T2T Apes

These are alignments of the T2T ape genomes described
in https://github.com/marbl/Primates. The manuscript is presently in preparation; please
read https://github.com/marbl/Primates#data-reuse-and-license
before downloading or using this data.

MAF track hub for 3 alignments referenced on primary assemblies
- https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/hubs/t2t-apes-2023v2-cactus-hub.txt
8-way primary progressive alignment.
- All steps to reproduce:
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/8-t2t-apes-2023v2/8-t2t-apes-2023v2.README.md
- HAL alignment (17 gigabytes)
  - URL: https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/8-t2t-apes-2023v2/8-t2t-apes-2023v2.hal
  - MD5: 9bd54385f6c8ff346bf5a781b7e4eacf
  - Newick tree: https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/8-t2t-apes-2023v2/8-t2t-apes-2023v2.nh
- All-to-all chains from the HAL alignments
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/8-t2t-apes-2023v2/chains/
- All data, including an MAF file referenced on each genome
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/8-t2t-apes-2023v2/
- CAT annotation results
  - CAT gene annotations v0.9
  - CAT gene annotations v1.0
16-way diploid progressive alignment. NOTE: diploid cactus is a work in progress, and coverage on chrX and chrY is about 5% lower than on the primary alignment.
- All steps to reproduce
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/16-t2t-apes-2023v2/16-t2t-apes-2023v2.README.md
- HAL alignment (33 gigabytes)
  - URL: https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/16-t2t-apes-2023v2/16-t2t-apes-2023v2.hal
  - MD5: c932a7ee2f83ed94d0d296d333c79371
- All-to-all chains from the HAL alignments
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/16-t2t-apes-2023v2/chains/
- All data, including a MAF file referenced on each primary or reference assembly
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/16-t2t-apes-2023v2/
10-way diploid mc pangenome alignment, including only human, chimp, bonobo, and gorilla.
- All steps to reproduce
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/10-t2t-apes-mc-2023v2/10-t2t-apes-mc-2023v2.README.md
- HAL alignment (13 gigabytes)
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/10-t2t-apes-mc-2023v2/10-t2t-apes-mc-2023v2.full.hal
  - MD5: d349b2e104b6437da34e5d8865cb136b
- All-to-all chains from the HAL alignments
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/10-t2t-apes-mc-2023v2/chains/
- All data, including pangenome graphs, indexes for mapping with vg giraffe, human-referenced VCF and MAF files
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/10-t2t-apes-mc-2023v2/
4-way diploid mc pangenome orang alignment (bornean and sumatran orangutans)
- All steps to reproduce
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/4-t2t-orangs-mc-2023v2/4-t2t-orangs-2023v2.pangenome.README.md
- HAL alignment (5.6 gigabytes)
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/4-t2t-orangs-mc-2023v2/4-t2t-orangs-mc-2023v2.full.hal
  - MD5: 2f6ecd379c2476e038be12acbf81eca6
- All-to-all chains from the HAL alignments
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/4-t2t-orangs-mc-2023v2/chains/
- All data, including pangenome graphs, indexes for mapping with vg giraffe, VCF and MAF files
  - https://cgl.gi.ucsc.edu/data/cactus/t2t-apes/4-t2t-orangs-mc-2023v2/

Contacts

Benedict Paten
Glenn Hickey
Mark Diekhans