SNP Projects

Required Schemes

In order to carry out SNP analysis, two schemes are required in the species database schemes table. Data is then stored in the assembly_lookup table to prevent duplication of jobs

  • snp_calls - Allows the gff file containing the SNPs to be stored for each assembly/reference combination
    • description snp_calls
    • name SNP Calls
    • param {“display”:”none”}
  • ref_masker - Allows the gff file containing the repeat regions for an assembly to be stored
    • description ref_masker
    • name Repeat Finder
    • param {“display”:”none”}
  • data_file contains the following json format
    • isolate A list of all metadata in the same format as MS Trees . The ID key refers to the node in the nwk tree , which is the assembly barcode