Central repository for whole genome Cactus alignments

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Whole genome alignments for mammals, fish, insects, grasses, cereals and more are now available via a central repository: https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/

We have centralised alignment files and metadata for the following groups:

  • Birds: Aves and its derived Fowl subalignment
  • Mammals: Mammals, Pigs, Rodents, Mice (UCSC), Humans (HPRC)
  • Insects: Coleoptera (beetles), Lepidoptera (moths and butterflies), Drosophila
  • Crustaceans: Crustacea
  • Nematodes: Nematoda (WormBase)
  • Plants (grasses/cereals): Barley, Rice, Wheat
  • Fish: Actinopterygii, Percomorpha, two AQUA-FAANG sets
  • Viruses: SARS-CoV-2

This collection includes a new alignment of 77 barley genomes produced with Minigraph-Cactus, complete with metadata on the barley assemblies, including the reference Morex, and cultivars such as Maximus, Bowman and Akashinriki.

These alignments may be used to compare synteny, translate coordinates, compare genome regions within and across the species represented therein. 

We aim to have more Cactus and other genome alignments ready to release in Spring 2027 onto the new Ensembl FTP – https://ftp.ebi.ac.uk/pub/ensemblorganisms/.