Resources

3K RG data
       The most comprehensive resource for re-sequenced rice genomes to-date is the 3,000 Rice Genomes project, a collaborative effort from BGI-Shenzhen, the Chinese Academy for Agricultural Sciences (CAAS), and IRRI.  The published datanote on the 3K RG dataset (The 3,000 rice genomes project) is available in GigaScience Journal. 

3K RG at AWS:   The Amazon Public Data program is hosting the 3K RG dataset (alignment to 5 published rice genomes, raw SNP and small indel calls from these alignments) , providing cloud-based infrastructure to make the dataset accessible and useable by  geneticists and breeders.

3K RG at DOST-ASTI:   In collaboration with the Philippines’ Department of Science and Technology Advanced Science and Technology Institute , the 3K RG analyzed data could be downloaded using two  file transfer methods, namely iRODS icommands , which is more for power users and developers, and offer greater  transfer speeds, and by WebDav , an extension to the popular HTTP protocol that web browsers use. Please see the iRODS instruction document for more details.

High Density Rice Array (HDRA) data
        Another resource with genotype information for 700,000 SNPs from a diverse set of rice accessions (among other datasets) is the NSF_ricediversity.org (McCouch et al, 2016) with > 1,600 genotyped accessions .  The list of the accessions for this project is available here.

Databases on the web

1. SNP-Seek : Hosts the complete genotyping information for the 3K RG Project (soon the HDRA and other projects too), as well as associated analyses tools, from IRIC.

2. RMBreeding : SNP and InDel database loaded with 3K RG data, from Rice Molecular Breeding & Molecular Genetics Group, Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences