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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 chromosome 1 | flapjack hapmap | cbsugobiizvm19:/share_data/test_data/lettuce/Lactuca__project1__2021-06-24__1152198variants__FLAPJACK.fjzip cbsugobiizvm19:/share_data/test_data/lettuce/Lactuca__project1__2021-06-24__1152198variants__HAPMAP.zip |
Actions:
- presentations on polyploid data
- user accounts for participants
- identify benchmarking criteria
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