Reference Disks in Terra
Terra now includes the ability to automatically attach a disk containing HG 19/HG 38 references to your Google Virtual Machine, saving time otherwise spent on potentially slow localization of large reference inputs. If the checkbox labeled ‘Use Reference Disks’ is selected, the execution engine will examine the inputs to a job to see if any of them correspond to reference inputs available on a reference disk image.
If this is the case, the engine will arrange for an additional disk to be mounted onto the VM using the reference disk image containing those inputs, allowing it to skip the delocalization process for the reference inputs. Currently two reference images are supported in Terra:
Reference Image Manifests
HG 19 public image
2020-10-26 (10 GiB)
gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai
gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict
gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt
gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi
gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta
HG 38 public images
We now have reference files for human genome assembly 38, release 27 for single cell pipelines., including hg38-sc-v27-mod which is a reference that has both intron and exon annotations. You can learn more about the tool that marks intronic regions here.
2020-10-26 (10 GiB)
gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai
gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list
gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz
gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt
gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac
gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa
gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.mu
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta
gs://gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.bed
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict
gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
hg38-sc-v27
gs://gcp-public-data--broad-references/hg38/v0/gencode.v27.primary_assembly.annotation.gtf
gs://gcp-public-data--broad-references/hg38/v0/GRCh38.primary_assembly.genome.fa
gs://gcp-public-data--broad-references/hg38/v0/star/star_2.7.9a_primary_gencode_human_v27.tar
hg38-sc-v27-mod
gs://gcp-public-data--broad-references/hg38/v0/single_nucleus/modified_gencode.v27.primary_assembly.annotation.gtf
gs://gcp-public-data--broad-references/hg38/v0/single_nucleus/modified_GRCh38.primary_assembly.genome.fa
gs://gcp-public-data--broad-references/hg38/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_human_v27.tar
M21 and M23 public images
The following M21 and M23 mouse reference files are used as inputs to WARP single-cell pipelines. See this document for more information. For more information regarding the use of the references, please see the overviews of Optimus and Smartseq2.
MM-10-sc
gs://gcp-public-data--broad-references/mm10/v0/GRCm38.primary_assembly.genome.fa
mm10-sc-vm21
gs://gcp-public-data--broad-references/mm10/v0/gencode.vM21.primary_assembly.annotation.gtf
gs://gcp-public-data--broad-references/mm10/v0/star/star_2.7.9a_primary_gencode_mouse_vM21.tar
gs://gcp-public-data--broad-references/mm10/v0/gencode.vM23.primary_assembly.annotation.gtf
gs://gcp-public-data--broad-references/mm10/v0/star/star_2.7.9a_primary_gencode_mouse_vM23.tar
mm10-sc-vm23-mod
gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf
gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_mm10.primary_assembly.genome.fa
gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar
While the reference disk feature should reduce the total time that the VM is running, it does increase the hourly rate of the VM since an additional disk is mounted to hold the reference image. For this reason ‘Use Reference Disks’ is turned off by default. Users should decide for themselves if it makes sense to trade off the decrease in time the VM is running for the increase in the VM’s hourly rate. If a job would spend a large proportion of its time localizing reference files relative to the time spent computing, the use of reference disks should be worthwhile.
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