illumina提供的打包好的参考序列、注释信息、index文件

Ensembl,NCBI,UCSC三大平台多个物种的全基因组参考序列、基因注释文件,还包括了BWA、Bowtie、Bowtie2的index文件。原网址为:http://support.illumina.com/sequencing/sequencing_software/igenome.html

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 Btau_4.6.1 Btau_4.2
UCSC bosTau7 bosTau6 bosTau4
Caenorhabditis elegans Ensembl WBcel235 WBcel215 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 Zv9
NCBI Zv9
UCSC danRer7
Drosophila melanogaster Ensembl BDGP5 BDGP5.25
NCBI build5.41 build5.3 build5 build4.1
UCSC 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 build37.2 build37.1 build36.3
UCSC 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_5.0 RGSC3.4
NCBI Rnor_5.0 RGSC_v3.4
UCSC 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