Ready-To-Use Reference Sequences and Annotations

The iGenomes are a collection of reference sequences and annotation files for commonly analyzed organisms. The files have been downloaded from Ensembl, NCBI, or UCSC, and chromosome names have been changed to be simple and consistent with their download source. Each iGenome is available as a compressed file that contains sequences and annotation files for a single genomic build of an organism.

For more information, see the iGenomes Overview and Change Log.

Species Source Build(s)      
Arabidopsis thaliana Ensembl TAIR10 TAIR9    
  NCBI TAIR10 build9.1    
Bacillus_cereus strain ATCC 10987 NCBI 2003-02-13      
Bacillus_subtilis strain 168 Ensembl EB2      
Bos taurus (Cow) Ensembl UMD3.1 Btau_4.0
  NCBI UMD_3.1.1 UMD_3.1 Btau_4.6.1 Btau_4.2
  UCSC bosTau8 bosTau7 bosTau6 bosTau4
Caenorhabditis elegans Ensembl WBcel235 WBcel215 WS220 WS210
  NCBI WS195 WS190    
  UCSC ce10 ce6    
Canis familiaris (Dog) Ensembl CanFam3.1 BROADD2    
  NCBI build3.1 build2.1    
  UCSC canFam3 canFam2    
Danio rerio (Zebrafish) Ensembl GRCz10 Zv9    
  NCBI GRCz10 Zv9    
  UCSC danRer10 danRer7    
Drosophila melanogaster Ensembl BDGP6 BDGP5 BDGP5.25  
  NCBI build5.41 build5.3 build5 build4.1
  UCSC dm6 dm3    
Enterobacteriophage lambda NCBI 1993-04-28      
Equus caballus (Horse) Ensembl EquCab2      
  NCBI EquCab2.0      
  UCSC equCab2      
Escherichia coli strain K12, DH10B Ensembl EB1      
  NCBI 2008-03-17      
Escherichia coli strain K12, MG1655 NCBI 2001-10-15      
Gallus gallus (Chicken) Ensembl Galgal4 WASHUC2    
  NCBI build3.1 build2.1    
  UCSC galGal4 galGal3    
Glycine max Ensembl Gm01      
Homo sapiens Ensembl GRCh37      
  NCBI GRCh38 build37.2 build37.1 build36.3
  UCSC hg38 hg19 hg18  
Macaca mulatta Ensembl Mmul_1      
Mus musculus (Mouse) Ensembl GRCm38 NCBIM37    
  NCBI GRCm38 build37.2 build37.1  
  UCSC mm10 mm9    
Mycobacterium tuberculosis strain H37Rv.EB1 Ensembl H37Rv.EB1      
  NCBI 2001-09-07      
Oryza sativa japonica (Rice) Ensembl IRGSP-1.0 MSU6    
Pan troglodytes (Chimpanzee) Ensembl CHIMP2.1.4 CHIMP2.1    
  NCBI build3.1 build2.1    
  UCSC panTro4 panTro3 panTro2  
PhiX Illumina RTA      
  NCBI 1993-04-28      
Pseudomonas aeruginosa strain PAO1 NCBI 2000-09-13      
Rattus norvegicus (Rat) Ensembl Rnor_6.0 Rnor_5.0 RGSC3.4  
  NCBI Rnor_6.0 Rnor_5.0 RGSC_v3.4  
  UCSC rn6 rn5 rn4  
Rhodobacter sphaeroides strain 2.4.1 NCBI 2005-10-07      
Saccharomyces cerevisiae (Yeast) Ensembl R64-1-1 EF4 EF3 EF2
  NCBI build3.1 build2.1    
  UCSC sacCer3 sacCer2    
Schizosaccharomyces pombe Ensembl EF2 EF1    
Sorangium cellulosum strain So_ce_56 NCBI 2007-11-27      
Sorghum bicolor Ensembl Sbi1      
Staphylococcus aureus strain NCTC 8325 NCBI 2006-02-13      
Sus scrofa (Pig) Ensembl Sscrofa10.2 Sscrofa9    
  NCBI Sscrofa10.2 Sscrofa10 Sscrofa9.2  
  UCSC susScr3 susScr2    
Zea mays (Corn) Ensembl AGPv3 AGPv2