Analysis Tools - developed by Rice Diversity

GWAS Pipeline

  • Description - The GWAS Pipeline was built in Python 2.6 and facilitates running GWAS. Given PLINK-formatted genotype and phenotype files, the pipeline will match them, apply filters, make kinship matrix and covariate files. Then the pipeline will run GWAS using linear mixed model(by EMMAX), and build Manhattan and QQ plots for each trait. In addition, the pipeline will also output a summary file showing only the most significant SNPs with allele effect calculated.
  • Download (Link data HDRA6.4_GWAS_pipeline.tar.gz)
  • Publication: McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J Open Access Resources for Genome Wide Association Mapping in Rice. Nature Comm, in press. (2016)

GWAS Viewer

  • Description - The GWAS Viewer is a web application to view –log p value data within a genomic context. It displays Os-Nipponbare-Reference-IRGSP-1.0/MSU7 gene annotation features, and each plotted point can reveal more information about the data value and related SNP (by clicking or hovering the mouse over the dot). It also includes hyperlinks to the Rice Diversity UCSC Genome Browser for closer examination of a SNP of interest within the genome annotation. The GWAS Viewer allows up to six plots to be loaded on-screen for any analysis that has been pre-loaded into the database, and plots can be zoomed synchronously for dynamic comparisons. The user can export and print any plots rendered in a session.
  • GWAS Viewer
  • • Publication: McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J Open Access Resources for Genome Wide Association Mapping in Rice. Nature Comm, in press. (2016)

Genome Browser

  • Description - We deployed a local mirror of the UCSC Genome Browser software (genome.ucsc.edu) for analysis of the HDRA SNP data in a genomic context. Both the Os-Nipponbare-Reference-IRGSP-1.0/MSU7 and the RAP-DB (rapdb.dna.affrc.go.jp) genome reference assemblies have been loaded. We created tracks for the HDRA SNP dataset, as well as for the Rice Diversity 44K SNP and 1536 SNP sets, and 384 OPA breeder’s mini-chips. We have adapted other browser format tracks to display SNP annotations such as putative amino acid changes and other functional annotations. In addition to the default tracks, users can create and load their own annotation tracks for displaying custom annotations and or datasets that map to the IRGSP-1.0 coordinates.
  • Download (Link data HDRA6.4_GWAS_pipeline.tar.gz)
  • Genome Browser
  • Publication: McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J Open Access Resources for Genome Wide Association Mapping in Rice. Nature Comm, in press. (2016)

Allele Finder

  • Description - The Allele Finder is a web application to retrieve genotypes by genomic location, for different sets of germplasm based on sample name or subpopulation. Alleles are displayed color-coded by nucleotide and can be masked out according to different attributes (e.g. mask/show heterozygous genotypes). Data is displayed to users in tabular form with genotypes encoded as A/G/C/T or A/B and can be exported or downloaded in plain-text format. The Allele Finder also displays MSUv7 gene models that are hyperlinked to our UCSC Genome Browser so the user can easily click for genomic context information.
  • Genome Browser
  • Publication: McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J Open Access Resources for Genome Wide Association Mapping in Rice. Nature Comm, in press. (2016)

ALCHEMY

Plumage

GBS PLAID

Rice Sub-population Viewer

  • Description: A browsable version of the Garris et. al figure.
  • Website

Seed Photo Library Viewer

  • Description: Photo viewer of seeds in the Rice Diversity germplasm collection
  • Website

PANorama

Other useful analysis tools and resources

  • PLINK - whole genome association analysis toolset
  • TASSEL - evaluates linkage disequilibrium, nucleotide diversity, and trait associations
  • Flapjack - graphical genotype and haplotype visualization
  • Gramene
    • Genetic Diversity module hosts RiceDiversity datasets as they are made publicly available. Gramene hosts a wealth of information about plant genes, proteins, QTL, regulatory pathways, markers, and maps.
    • SNP Query - useful tool viewing and querying by SNP location and germplasm
    • Web launch TASSEL - Gramene Diversity data sets automatically loaded in a live-launch of TASSEL
  • BLAST - several rice genome assemblies available for BLAST analysis
  • ClustalW2 - multiple sequence alignment tool
  • r/QTL mapping script - automated QTL mapping script used in Spindel and Wright et al., 2013