iGenomes

To make the use of reference genomes easier, Illumina has developed a centralized resource called iGenomes. The most commonly used reference genome files are organized in a consistent structure for multiple genomes.

We have downloaded a copy of iGenomes onto our clusters, and developed them into environment modules to make them easy to use.

Link to section 'AGPv3' of 'iGenomes' AGPv3

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/AGPv3

Link to section 'BDGP6' of 'iGenomes' BDGP6

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/BDGP6

Link to section 'bosTau8' of 'iGenomes' bosTau8

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/bosTau8

Link to section 'canFam3' of 'iGenomes' canFam3

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/canFam3

Link to section 'CanFam3.1' of 'iGenomes' CanFam3.1

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Gene annotation files were downloaded from Ensembl release 81. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/CanFam3.1

Link to section 'ce10' of 'iGenomes' ce10

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/ce10

Link to section 'CHIMP2.1.4' of 'iGenomes' CHIMP2.1.4

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/CHIMP2.1.4

Link to section 'danRer10' of 'iGenomes' danRer10

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/danRer10

Link to section 'dm6' of 'iGenomes' dm6

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/dm6

Link to section 'EB1' of 'iGenomes' EB1

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Gene annotation files were downloaded from EnsemblGenomes release 27. Ensembl now uses the name 'ASM1942v1, June 2008' for this assembly.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/EB1

Link to section 'EB2' of 'iGenomes' EB2

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Gene annotation files were downloaded from EnsemblGenomes release 27.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/EB2

Link to section 'EF2' of 'iGenomes' EF2

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Annotation files in this directory and subdirectories were downloaded from EnsemblGenomes release 27. Ensembl now uses the name 'ASM294v2, May 2009' for this assembly.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/EF2

Link to section 'equCab2' of 'iGenomes' equCab2

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/equCab2

Link to section 'EquCab2' of 'iGenomes' EquCab2

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/EquCab2

Link to section 'galGal4' of 'iGenomes' galGal4

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/galGal4

Link to section 'Galgal4' of 'iGenomes' Galgal4

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Galgal4

Link to section 'Gm01' of 'iGenomes' Gm01

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Gm01

Link to section 'GRCh37' of 'iGenomes' GRCh37

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Gene annotation files were downloaded from Ensembl release 75. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/GRCh37

Link to section 'GRCh38' of 'iGenomes' GRCh38

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/GRCh38

Link to section 'GRCm38' of 'iGenomes' GRCm38

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/GRCm38

Link to section 'GRCz10' of 'iGenomes' GRCz10

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/GRCz10

Link to section 'hg19' of 'iGenomes' hg19

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/hg19

Link to section 'hg38' of 'iGenomes' hg38

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/hg38

Link to section 'IRGSP-1.0' of 'iGenomes' IRGSP-1.0

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/IRGSP-1.0

Link to section 'mm10' of 'iGenomes' mm10

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/mm10

Link to section 'Mmul_1' of 'iGenomes' Mmul_1

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Mmul_1

Link to section 'panTro4' of 'iGenomes' panTro4

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/panTro4

Link to section 'R64-1-1' of 'iGenomes' R64-1-1

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/R64-1-1

Link to section 'rn6' of 'iGenomes' rn6

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/rn6

Link to section 'Rnor_5.0' of 'iGenomes' Rnor_5.0

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Rnor_5.0

Link to section 'Rnor_6.0' of 'iGenomes' Rnor_6.0

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Rnor_6.0

Link to section 'sacCer3' of 'iGenomes' sacCer3

The contents of this directory were downloaded from UCSC on: March 6, 2013 local modroot="/depot/itap/datasets/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3"

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/sacCer3

Link to section 'Sbi1' of 'iGenomes' Sbi1

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Sbi1

Link to section 'Sscrofa10.2' of 'iGenomes' Sscrofa10.2

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/Sscrofa10.2

Link to section 'susScr3' of 'iGenomes' susScr3

The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/susScr3

Link to section 'TAIR10' of 'iGenomes' TAIR10

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015. Gene annotation files were downloaded from EnsemblGenomes release 27. SmallRNA annotation files were downloaded from miRBase release 21.

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/TAIR10

Link to section 'UMD3.1' of 'iGenomes' UMD3.1

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/UMD3.1

Link to section 'WBcel235' of 'iGenomes' WBcel235

Link to section 'Module' of 'iGenomes' Module

You can load the modules by:

module load datasets
module load igenomes/WBcel235