Cactus Alignment Track Settings

Cactus Alignment (All Comparative Genomics tracks)

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All	*track Type*	Alignments
*Organisms*
hs1
hg38

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	Hide Configure	hg38	Cactus GRCh37/hg38	Data format
	Hide Configure	CHM13/hs1	Cactus CHM13/hs1	Data format

Data schema/format description and download

Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1)

Description

Cactus reference-free alignments of GRCh38 and T2T CHM13 v2.0, using chimp (GCF_002880755.1/panTro6) as an out-group.

Display Conventions and Configuration

This track uses the Snake tracks display conventions and configuration.

Methods

Alignments were generated using the Cactus reference alignment package and are stored as a HAL file.

Data Access

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.

Credits

This track was created by Marina Haukness <mhauknes@ucsc.edu> if the UC Santa Cruz Computational Genomics Lab.

References

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