Genomics data

This article is a draft

This is not a complete article: This is a Draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

In partnership with C3G, we maintain several genome databases that are available on Compute Canada's general purpose clusters (Béluga, Cedar, Graham). In addition to the FASTA sequence, many genomes include aligner indices and annotation files.

When it is available, the genomics data are always located here: /cvmfs/ref.mugqic/genomes.

We encourage you to browse the directory to get more information.

[user@cedar5 ~]$  ls -1 /cvmfs/ref.mugqic/genomes
blast_db
chimera_gold_db
chimera_unite_db
greengenes_db
mirbase
pfam_db
silva_db
species
temp
unite_db

Available genomes in species/

Common name	Species	Builds
Human	Homo sapiens	GRCh38 GRCh37 hg19
Mouse	Mus musculus	GRCm38 mm10 mm9 NCBIM37
Rat	Rattus norvegicus	rn5 Rnor_5.0 Rnor_6.0
Monkey	Macaca mulatta	MMUL_1
Chimpanzee	Pan troglodytes	panTro4 CHIMP2.1.4
Baboon	Papio anubis	PapAnu2.0
Dog	Canis familiaris	CanFam3.1
Cow	Bos taurus	UMD3.1
Chicken	Gallus gallus	Galgal4
Fly	Drosophila melanogaster	BDGP5
C. Elegans	Caenorhabditis elegans	WBcel235
Yeast	Saccharomyces cerevisiae	R64-1-1
	Schizosaccharomyces pombe	ASM294v2
Bacteria	Escherichia coli str k_12 substr dh10b	ASM1942v1
	pseudomonas aeruginosa pa14	Pseu aeru PA14_V1
	Pseudomonas aeruginosa UCBPP_PA14	ASM1462v1
Plants	Arabidopsis thaliana	TAIR10