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”}
{
"microreact_data:
{
"url":"http:\/\/microreact.org\/project\/r1GfN0ufg",
"short_id":"r1GfN0ufg"
},
"matrix":"\/share_space\/interact\/outputs\/1794\/1794930\/test_mr_snp_1.aln.matrix.gz",
"parent_workspace":"2698",
"snp_count":
{
"77580":1297,
"69837":2771,
......,
"7021":"ESC_FA7021AA_AS"
},
"processing_matrix":"true",
"processing":"true",
"ref_id":57021,
"profiles":"\/share_space\/snps\/ecoli\/55\/2699\/profiles.json",
"snp_fasta":"\/share_space\/snps\/ecoli\/55\/2699\/snps.fasta",
"raxml_tree":"\/share_space\/interact\/outputs\/1794\/1794931\/test_mr_snp_1.rooted.nwk",
"assembly_ids":[69396,81488,25374,19187,77580,77672,22907,26316,69835,69837],
"complete":"true",
"data_file":"/path_to_data/33.json"
}
- 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