Several of these files are in tar.gz format. To extract the files on a Windows system, use 7zip in administrator mode.
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. Chromosome names have been changed to be simple and consistent with the 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.
| Species | Source | Build(s) | |||
|---|---|---|---|---|---|
| Arabidopsis thaliana | Ensembl | TAIR10 | TAIR9 | ||
| NCBI | TAIR10 | ||||
| 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 | galGal5 | galGal4 | galGal3 | ||
| Glycine max | Ensembl | Gm01 | |||
| Homo sapiens | Ensembl | GRCh37 | |||
| NCBI |
|
build37.2 | build37.1 | build36.3 | |
| UCSC | hg38 | hg19–Does not have annotation files. |
hg18 | ||
| DRAGEN Graph | GRCh37d5 | hg19 | hg38 | ||
| 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 | Sscrofa11.1 | Sscrofa10.2 | Sscrofa9 | |
| NCBI | Sscrofa10.2 | Sscrofa10 | Sscrofa9.2 | ||
| UCSC | susScr3 | susScr2 | |||
| Zea mays (Corn) | Ensembl | AGPv4 | AGPv3 | AGPv2 | |