Genomes

The CARC provides a set of ready-to-use reference sequences and annotations for commonly analyzed organisms in a directory accessible from the Discovery and Endeavour clusters.

The reference genomes are sourced from iGenomes, a project by Illumina to provide ready-to-use genome assemblies and annotations from Ensembl, NCBI, and UCSC. Each genome directory contains index files of the whole genome for use with the BWA, Bowtie, and Bowtie2 aligners.

To access the genomes below, click the genome and format of your choice, then click the clipboard icon to copy the on-disk location. You can then paste it in your submission scripts to use in your analysis.

OrganismSourceBuild
AbundantSequencesBWAIndexBowtie2IndexBowtieIndexChromosomesWholeGenomeFastaMethylationWholeGenomeFasta
Arabidopsis thaliana

Ensembl

NCBI

TAIR10

TAIR9

TAIR10

build9.1

Bacillus cereus ATCC 10987

NCBI

2004-02-13

Bacillus subtilis 168

Ensembl

EB2

Bos taurus

NCBI

UCSC

Ensembl

UMD_3.1

UMD_3.1.1

Btau_4.2

Btau_4.6.1

bosTau7

bosTau4

bosTau6

bosTau8

UMD3.1

Btau_4.0

Caenorhabditis elegans

Ensembl

UCSC

NCBI

WBcel215

WS220

WS210

WBcel235

ce10

ce6

WS195

WS190

Canis familiaris

NCBI

UCSC

Ensembl

build3.1

build2.1

canFam2

canFam3

BROADD2

CanFam3.1

Danio rerio

UCSC

Ensembl

NCBI

danRer10

danRer7

GRCz10

Zv9

GRCz10

Zv9

Drosophila melanogaster

UCSC

Ensembl

NCBI

dm6

dm3

BDGP5

BDGP6

BDGP5.25

build5.41

build5

build5.3

build4.1

Enterobacteriophage lambda

NCBI

1993-04-28

Equus caballus

Ensembl

NCBI

UCSC

EquCab2

EquCab2.0

equCab2

Escherichia coli K 12 DH10B

Ensembl

NCBI

EB1

2008-03-17

Escherichia coli K 12 MG1655

NCBI

2001-10-15

Gallus gallus

Ensembl

NCBI

UCSC

Galgal4

WASHUC2

build2.1

build3.1

galGal4

galGal5

Glycine max

Ensembl

Gm01

Homo sapiens

UCSC

NCBI

Ensembl

hg19

hg38

GRCh38

build36.3

build37.1

build37.2

GRCh37

Macaca mulatta

Ensembl

Mmul_1

Mus musculus

UCSC

NCBI

Ensembl

mm10

mm9

build37.1

GRCm38

GRCm38

NCBIM37

Mycobacterium tuberculosis H37RV

NCBI

Ensembl

2001-09-07

H37Rv.EB1

Oryza sativa japonica

Ensembl

IRGSP-1.0

MSU6

Pan troglodytes

UCSC

Ensembl

NCBI

panTro4

panTro3

panTro2

CHIMP2.1

CHIMP2.1.4

build3.1

build2.1

PhiX

Illumina

NCBI

RTA

1993-04-28

Pseudomonas aeruginosa PAO1

NCBI

2000-09-13

Rattus norvegicus

Ensembl

NCBI

UCSC

RGSC3.4

Rnor_6.0

Rnor_5.0

Rnor_6.0

Rnor_5.0

RGSC_v3.4

rn5

rn6

rn4

Rhodobacter sphaeroides 2.4.1

NCBI

2005-10-07

Saccharomyces cerevisiae

UCSC

Ensembl

NCBI

sacCer2

R64-1-1

EF2

EF3

EF4

build3.1

build2.1

Schizosaccharomyces pombe

Ensembl

EF2

EF1

Sorangium cellulosum So ce 56

NCBI

2007-11-27

Sorghum bicolor

Ensembl

Sbi1

Staphylococcus aureus NCTC 8325

NCBI

2006-02-13

Sus scrofa

NCBI

Ensembl

UCSC

Sscrofa10

Sscrofa10.2

Sscrofa9.2

Sscrofa11.1

susScr2

susScr3

Zea mays

Ensembl

AGPv4

AGPv3

AGPv2

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