Contents
| Table of Contents | ||||||
|---|---|---|---|---|---|---|
|
Genotyping data management systems
System | Group |
|---|
Contact | VM Hostname | phase | |
|---|---|---|---|
JHI |
MontyDB
Cornell
Francisco
GDM
Cornell
| ||||||||||
Cornell GOBii |
| |||||||||
CIRAD |
| |||||||||
BTI |
Ask Titima
Gigwa
CIRAD
| ||||||||||
MontyDB | Cornell McCouch Lab |
| ||||||||
Broad Institute |
| |||||||||
Cornell Buckler Lab | Ask Ed |
BCF
| ||||||||
Breeding Insight |
| |||||||
University of Washington | Dori? |
|
Patrick
| ||||||||
Patrick |
|
VM allocations
VM Hostname | Status | Server Pool | Assignment | username | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| cbsugobii09 | Breedbase | breedbase | |||||||
| cbsugobii09 | GDM | gadm | |||||||
| cbsugobii10 | Gigwa | gigwa | |||||||
| cbsugobii10 | PHG | phg | |||||||
| cbsugobii11 | Germinate | jhi | |||||||
| 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 Hapmap: cbsugobiizvm19:/shared_data/test_data/genomics-systems-comparison/rice/Dataset.hmp.txt | ||||
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 |
|
|
|
|
|
|
|
|
|
| |||||||
potato (polyploid) | VCF |
|