GenPipes Genome 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