GenPipes Genome resources

C3G, in partnership with Compute Canada, maintains several genomes that are available on several HPC centres including Beluga, Cedar and others. 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