Cactus Alignment Track Settings

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Cactus Alignment (All Comparative Genomics tracks)

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

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.

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.

This track was created by Marina Haukness <[email protected]> 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