About

The Rice SNP-Seek Database and Web applications are developed using both open-source and commercial softwares.

Data Generation

  1. BWA-MEM

  2. GATK

  3. VISTA

Storage

  1. Oracle

  2. PostgreSQL

  3. HDF5

Web-application

  1. Hibernate

  2. Spring

  3. ZK

  4. JBrowse

  5. BioJava

  6. jsphySVG

Development

  1. MyEclipse

  2. Read the Docs

  3. GitHub

  4. Docker

Publications

Primary publication

  • Mansueto, et al. Rice SNP-seek database update: new SNPs, indels, and queries.Nucl. Acids Res.(2017) 45 (D1): D1075-D1081. doi: 10.1093/nar/gkw1135
    This paper describes new features and datasets added to SNP-Seek in 2015-2017 as well as software and database updates.

Other publications

  • Mansueto, et al. SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa.Current Plant Biology(2016). 7-8:16-25 doi: 10.1016/j.cpb.2016.12.003
    This paper contains details on variant calling for 5 references, integration of additional genomic data, web interface, database schema, use cases, web services API.

  • Alexandrov, et al. SNP-Seek database of SNPs derived from 3000 rice genomes.Nucl. Acids Res.(2015). 43(D1):D1023-D1027 doi: 10.1093/nar/gku1039
    This is the first publication introducing SNP-Seek database, data generation for Nipponbare reference,and common use cases.

  • Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature.(2018). 557:43-49 doi: 10.1038/s41586-018-0063-9
    The main scientific paper for the 3K RGP.