Genotyping data management systems
System | Group/Institution | Contact |
|---|---|---|
Germinate | JHI | Sebastian |
MontyDB | Cornell | Francisco |
GDM | Cornell | Joel |
Breedbase | BTI | Ask Titima |
Gigwa | CIRAD | Guilhem |
PHG | Cornell | Ask Ed |
BCF | Broad Institute | |
GDR-BIMS (https://github.com/laceysanderson ) | Un. of Washington | Dori? |
Patrick |
VM allocations
VM Hostname | Status | Server Pool | Assignment | username |
|---|---|---|---|---|
OFF | cbsugobii09 | Breedbase | breedbase | |
ON | cbsugobii09 | GDM | gadm | |
ON | cbsugobii10 | Gigwa | gigwa | |
OFF | cbsugobii10 | PHG | phg | |
ON | cbsugobii11 | Germinate | jhi | |
OFF | cbsugobii11 | MontyDB | montydb |
Each VM has the following resources:
8 CPUs
64 GB RAM
2 TB SSD
/storage mounted volume
/shared_data mounted volume
Users
Username | User |
|---|---|
gadm | system |
yaw | |
dave | |
francisco |
Datasets
Dataset | Format | Location |
|---|---|---|
Maize NAM | CSV | /shared_data/test_data/NAM_HM32/csv |
Simulated datasets | ||
polyploid data in VCF | Moira share a dataset - invite to next meeting | |
indel data | ||
rice high density array | vcf | The Rice High Density Array is : 700K SNPs x ~1500 samples SNPs only vcf too Francisco loaded to Gigwa (own instance) already no problem http://rs-bt-mccouch4.biotech.cornell.edu/staged_data/CSHL_EVA_Release_HDRA.tar |
African rice | https://gigwa.ird.fr/gigwa/?module=AfricanRice available as vcf metadata availability? | |
3,000 rice genomes | too large? 29M SNPs | |
lettuce Wageningen Public dataset | vcf | 12M markers x 500 accessions 3 vcfs - one SNPs, one indels, one structural variants 40 GBs https://www.nature.com/articles/s41588-021-00831-0/pub/CNSA/data2/CNP0000335/Other/variation |
Lettuce | hapmap flapjack | cbsugobiizvm19:
/shared_data/test_data/genomics-systems-comparison/lettuce/
chr1/
Lactuca__project1__2021-06-24__1152198variants__FLAPJACK.fjzip
Lactuca__project1__2021-06-24__1152198variants__HAPMAP.zip
markerlists.zip
full/
Lactuca__project1__2021-06-28__12983735variants__FLAPJACK.fjzip
Lactuca__project1__2021-06-28__12983735variants__HAPMAP.zip
|