Bioinformatics resources

 
 

C3G, in partnership with Compute Canada, maintains several genomes that are available on several HPC centres including Guillimin, Cedar, Graham and Mammouth. In addition to the fasta sequence, many genomes include aligner indices and annotation files.

 

To access these genomes, you need to add the following lines to your .bashrc file.

## GenPipes/MUGQIC genomes and modules
export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6

 

To explore the available genomes, you can type:

ls $MUGQIC_INSTALL_HOME/genomes/species/

 
 

Available Genomes

 

Human
Species: Homo_sapiens
Available builds: GRCh38, GRCh37, hg19

Mouse
species: Mus_musculus
Available builds: GRCm38, mm10, mm9, NCBIM37

Rat
Species: Rattus_norvegicus
Available builds: rn5, Rnor_5.0, Rnor_6.0

Monkey
Species: Macaca_mulatta
Available builds: MMUL_1

Chimpanzee
Species: Pan_troglodytes
Available builds: panTro4, CHIMP2.1.4

Baboon
Species: Papio_anubis
Available builds: PapAnu2.0

Dog
Species: Canis_familiaris
Available builds: CanFam3.1

Cow
Species: Bos_taurus
Available builds: UMD3.1

Chicken
Species: Gallus_gallus
Available builds: Galgal4

Fly
Species: Drosophila_melanogaster
Available builds: BDGP5

C. Elegans
Species: Caenorhabditis_elegans
Available builds: WBcel235

Yeast
Species: Saccharomyces_cerevisiae
Available builds: R64-1-1
Species: Schizosaccharomyces_pombe
Available builds: ASM294v2

Bacteria
Species: Escherichia_coli_str_k_12_substr_dh10b
Available builds: ASM1942v1
Species: pseudomonas_aeruginosa_pa14
Available builds: Pseu_aeru_PA14_V1
Species: Pseudomonas_aeruginosa_UCBPP_PA14
Available builds: ASM1462v1

Plants
Species: Arabidopsis_thaliana
Available builds: TAIR10