Cactus reference-free alignments of GRCh38 and T2T CHM13 v2.0, using chimp (GCF_002880755.1/panTro6) as an out-group.
This track uses the Snake tracks display conventions and configuration.
Alignments were generated using the Cactus reference alignment package and are stored as a HAL file.
The alignment summary can be explored interactively with the Table Browser or the Data Integrator.
The full multiple alignment is stored as a HAL file that can be downloaded from our download server as t2tChm13.v2.0.hal. HAL files can be queried and converted with the tools in the HAL toolkit.
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.
This track was created by Marina Haukness <mhauknes@ucsc.edu> if the UC Santa Cruz Computational Genomics Lab.
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. PMID: 33177663; PMC: PMC7673649
Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013 May 15;29(10):1341-2. PMID: 23505295; PMC: PMC3654707