T3Pio_Data_README

# GWA Data and References

##Data Set Location
1. /scicomp/groups/OID/NCEZID/DFWED/EDLB/projects/T3Pio_Data

##Design Set
1. 19 genomes used in designing the current set of primers
   1. Represent the most common outbreak Salmonella strains

##DesignSpecFilMultifasta
1. Amplicons generated from the version 0.3 pipeline run on the 19 design isolates
   1. Uses the shared primers from blastANI and stoolbugs specificity testing

##Metagenomes
1. COAL set genomes in the BlastANI approach
   1. Primer set was used in in silico PCR
   2. blast was then used to identify the generated amplicons as pertaining to salmonella of non-salmonella specific targets

##MasterPrimerFile
1. List of the identified shared primers from the blastANI approach and stoolbug (JulieBugs) testing
2. From the pipeline version 0.3

##Sal_26_genome_serotypes
1. List of the serotypes used in both the design and validation set

##SpecSharedPrimersValFasta
1. Amplicons generated from the version 0.3 pipeline run on the 266 validation isolates
   1. Represents the diversity of salmonella serotypes

##StoolBugMultiFastas(JulieBugs)
1. Set of 330 genomes of commonly found bacteria in stool
   1. Used to help identify salmonella specific primers in conjuction with the blastANI approach

##ValidationSet
1. Set of 266 salmonella isolates used in validation of the primer MLST scheme

##ValidationSpecFilMultifasta
1. Amplicons generated from the version 0.3 pipeline run on the 266 validation isolates
   1. Uses the shared primers from blastANI and stoolbugs (JulieBugs) specificity testing