PrimerSet0.2CreationMethods

Outline:
1.Design Set Creation
    1.1.Why these isolates chosen
    1.2.Which isolates were chosen
    1.3.Location of isolate assemblies and GBK files
            Located on the GWA projects\T3Pio_Data\DesignSet
        1.3.1.How the GBK files were created
2.Validation Set Creation
    2.1.Why these isolates chosen
    2.2.Which isolates were chosen
    2.3.Location of isolate assemblies and GBK files
        2.3.1.How the GBK files were created
3.Orthofinder
    3.1.How orthofinder works
    3.2.What we put into orthofinder
    3.3.Orthogroup selection
        3.3.1.What orthogroups we included
        3.3.2.Selection process
4.Multifasta Creation
    4.1.How the multifasta files were generated
5.MUSCLE
    5.1.How the alignment files were generated
6.TrimAl
    6.1.What the trimming parameters were for the alignment files
7.EMBOSS consambig
    7.1.What the consensus file creation parameters were
8.Primer3
    8.1.What the primer creation specifications were
    8.2.How primers were filtered
9.EMBOSS PrimerSearch
    9.1.What were the primersearch parameters
    9.2.Primersearch file validation
    9.3.Primersearch parsing
        9.3.1.Multifasta generation from primersearch results
10.Specificity Testing
    10.1.BlastANI process
        10.1.1.COAL metagenome set
            Outbreak set of isolates
        10.1.2.BlastANI process
    10.2.Stool Bugs
        10.2.1.Stool bug generation process
        10.2.2.Primersearch against stool bugs
    10.3.Overlap primers
        10.3.1.Finding primers passing in both BlastANI and stool bug specificity approaches