CLC reference genomes

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Within the CLC genomics server, we created a shared data location called CLC_REFERENCE_GENOMES, where we plan to provide reference data for model organisms, that may be useful for a larger number of CLC users. This way users don't have to download reference data themselves and we can avoid having multiple redundant copies the same data.

The table gives an overview on the available files in the CLC_REFERENCE_GENOMES data location and the original files they have been created from, as well as a link to the original repository and the creation date of the build.

Species Build Files in CLC Created from Download location Build date
Arabidopsis Thaliana TAIR10 TAIR10_sequence

TAIR10_chr{1-5}.fas
TAIR10_chrC.fas
TAIR10_chrM.fas

ftp.arabidopsis.org 26 Nov 2014 14:22:09

TAIR10_Chromosome
TAIR10_exon
TAIR10_Exon
TAIR10_gene-1
TAIR10_gene
TAIR10_Gene
TAIR10_miRNA
TAIR10_mRNA
TAIR10_Ncrna
TAIR10_Protein
TAIR10_Pseudogene
TAIR10_rRNA
TAIR10_snoRNA
TAIR10_snRNA
TAIR10_transcript
TAIR10_tRNA
TAIR10_utr-1
TAIR10_utr

TAIR10_GFF3_genes.gff ftp.arabidopsis.org 26 Nov 2014 14:25:03
Mus Musculus GRCm38 GRCm38_sequence

Mus_musculus.GRCm38.dna.chromosome.{1-19}.fa.gz
Mus_musculus.GRCm38.dna.chromosome.X.fa.gz
Mus_musculus.GRCm38.dna.chromosome.Y.fa.gz
Mus_musculus.GRCm38.dna.chromosome.MT.fa.gz

ftp.ensembl.org 27 Nov 2014 09:05:47
GRCm38_variants Mus_musculus.gvf.gz ftp.ensembl.org 27 Nov 2014 09:55:51

GRCm38_CDS
GRCm38_Exon
GRCm38_Gene
GRCm38_mRNA
GRCm38_Selenocysteine
GRCm38_Transcript
GRCm38_Utr

Mus_musculus.GRCm38.77.gtf.gz ftp.ensembl.org 27 Nov 2014 09:13:18
Homo Sapiens hg19 hg19_sequence

Homo_sapiens.GRCh37.75.dna.chromosome.{1-22}.fa.gz
Homo_sapiens.GRCh37.75.dna.chromosome.X.fa.gz
Homo_sapiens.GRCh37.75.dna.chromosome.Y.fa.gz
Homo_sapiens.GRCh37.75.dna.chromosome.MT.fa.gz

ftp.ensembl.org 27 Nov 2014 15:22:01
hg19_dbsnp variants snp138.txt.gz hgdownload.cse.ucsc.edu 01 Dez 2014 15:11:03
hg19_dbsnp (common) variants snp138Common.txt.gz hgdownload.cse.ucsc.edu 01 Dez 2014 09:52:35

hg19_CDS
hg19_Exon
hg19_Gene
hg19_mRNA
hg19_Selenocysteine
hg19_Transcript
hg19_Utr

Homo_sapiens.GRCh37.75.gtf.gz ftp.ensembl.org 27 Nov 2014 15:32:25