@article{fdi:010076213,
  title = {{R}ice {G}alaxy : an open resource for plant science},
  author = {{J}uanillas, {V}. and {D}ereeper, {A}lexis and {B}eaume, {N}. and {D}roc, {G}. and {D}izon, {J}. and {M}endoza, {J}. {R}. and {P}erdon, {J}. {P}. and {M}ansueto, {L}. and {T}riplett, {L}. and {L}ang, {J}. and {Z}hou, {G}. and {R}atharanjan, {K}. and {P}lale, {B}. and {H}aga, {J}. and {L}each, {J}. {E}. and {R}uiz, {M}. and {T}homson, {M}. and {A}lexandrov, {N}. and {L}armande, {P}ierre and {K}retzschmar, {T}. and {M}auleon, {R}. {P}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {R}ice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. {G}ermplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. {C}ombining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. {C}omparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. {A}nalyses involving {DNA} sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers. {F}indings: {T}he {R}ice {G}alaxy resource has shared datasets that include high-density genotypes from the 3,000 {R}ice {G}enomes project and sequences with corresponding annotations from 9 published rice genomes. {T}he {R}ice {G}alaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. {A} prototype {R}ice {G}alaxy compliant to {O}pen {A}ccess, {O}pen {D}ata, and {F}indable, {A}ccessible, {I}nteroperable, and {R}eproducible principles is also presented. {C}onclusions: {R}ice {G}alaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.},
  keywords = {rice ; breeding ; workflow ; genomes ; high-density genotypes ; reproducibility ; single-nucleotide polymorphism ; genome-wide association studies ; {G}alaxy project},
  booktitle = {},
  journal = {{G}igascience},
  volume = {8},
  numero = {5},
  pages = {giz028 [14 p.]},
  ISSN = {2047-217{X}},
  year = {2019},
  DOI = {10.1093/gigascience/giz028},
  URL = {https://www.documentation.ird.fr/hor/fdi:010076213},
}