The EquCab3 assembly(PMID:30456315) plus the Male Specific Y chromosome (MH341179.1 PMID:30054462).
    Provided are FASTA formatted files as well as annotation from UCSC Golden Path, NCBI RefSeq, and ENSEMBL.
    Files can be accessed either by "Right clicking" (Ctrl-click on a Mac) to download the linked file,
    or by using wget or curl on the copied URL at the unix/linux command line.
Source Fasta File Gene Annotation
UCSC Golden Path EquCab3(+MSY) goldenPath.Ec_build-3.0_wMSY.fa goldenPath.Ec_build-3.0.ensGene._wMSY.gtf goldenPath.Ec_build-3.0.ncbiRefSeq_wMSY.gtf
ENSEMBLE EquCab3(+MSY) ensembl.Ec_build-3.0.wMSY.fa ensembl.Ec_build-3.0.wMSY.gtf
NCBI RefSeq EquCab3(+MSY) ncbi.Ec_build-3.0.wMSY.fa ncbi.Ec_build-3.0.wMSY.gff 

  Single Nucleotide Polymorphism data generated from 101 Japanese Thoroughbreds (Tozake et al., PMID:34362995) 
  
  (VCF file)
  (VCF index)


  Catalog of SNP and small structural variation generated from 534 horses across >40 breeds (Durward-Akhurst et al.,  PMID: 34925451  PMCID: PMC8676274) 
  (VCF file)
  (VCF index)


  VCF files for PAG 2023 Hands on Equine Genomics Workshop
  (UMN horse VCF subset file for demo.)
  (UMN horse VCF subset index file for demo.)

  (UMN Quarterhorse VCF subset file for demo.)
  (UMN Quarterhorse VCF subset index file for demo.)

  (UMN dataset breed information)

  BED files for PAG 2023 Hands on Equine Genomics Workshop
  (H3K4me1 Muscle Peaks for demo.)
  (index.)