SMAP design

    Scope & Quick Start
        Scope
        Guidelines for sgRNA design with CRISPOR
        Quick Start and options
            Mandatory arguments
            General Options
                general options
                amplicon filter options
                guide filter options
                guide-amplicon overlap filter options
        Output
            graphical output
            tabular output
            gff output
    
    Feature Description
        Definition of reference gene, CDS, amplicons, guides, and overlaps
        Including polymorphisms during amplicon design
    
    How It Works
        Preparing reference gene sets
        Step 1. Positioning guides
        Step 2. Designing amplicons
        Step 3. Overlapping guides and amplicons
        Step 4. Ranking amplicons
        Step 5. Selecting amplicons and guides
        
    Example Data
        Illustration of primer and sgRNA design
            small divergent gene family
            large and conserved gene family
            small gene family in heterozygous species
    
    Recommendations & Troubleshooting
        Picking reference sequences for primer design
            group by HOMOLOGY
            group by INTERPRO
            group by PATHWAY    
        Specificity and coverage of primer designs versus completeness in the reference gene set
        Primer designs for specific sequencing technologies
            HiPlex amplicon sequening HiSeq
            Multiplex amplicon sequencing MiSeq: 
            Singleplex amplicon sequencing Sanger, Ice/Tide
            LongRange PCR, MinION (?)
        Troubleshooting
    
    Summary of Commands
        Mandatory arguments
        General Options
            general options
            amplicon filter options
            guide filter options
            guide-amplicon overlap filter options