Cactus Alignment Track Settings
 
Cactus Alignment   (All Comparative Genomics tracks)

Maximum display mode:       Reset to defaults   
Select track Type (Help):
Alignments ▾      
Select subtracks by track type and organisms:
 All track Type Alignments 
Organisms
hs1 
hg38 
List subtracks: only selected/visible    all  
 
hide
 Configure
 hg38  Cactus GRCh37/hg38   Schema 
 
hide
 Configure
 CHM13/hs1  Cactus CHM13/hs1   Schema 

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.

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