openPrimeR-package: Multiplex PCR Primer Design and Analysis.
In openPrimeR: Multiplex PCR Primer Design and Analysis

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With openPrimeR you can evaluate existing primers or design novel primers for multiplex polymerase chain reaction that are optimized with respect to the coverage of template sequences and the physicochemical properties of the primers.

For designing primers, you just need the function design_primers from openPrimeR. As a minimal input, this function requires:

A set of template sequences: You an load a Templates object with read_templates.
Settings for primer design: You can load a DesignSettings object from a (supplied) XML file with read_settings. The settings can be easily customized using the setters constraints, constraintLimits, cvg_constraints, conOptions, and PCR.

For evaluating existing primers you can load a FASTA or CSV file containing the primers and templates of of interest using read_primers and read_templates, respectively. After evaluating the properties of the primers using check_constraints, you can interpret the results with several functions. For example, you can analyze the coverage of the template sequences using get_cvg_stats, determine the deviation from the target constraints using plot_constraint_deviation, or create a comprehensive report on the analyzed primers using create_report. In order to compare several primer sets with each other, you can create a table of the properties of the primer sets using get_comparison_table or create a full report, again using create_report.

openPrimeR uses the following options:

openPrimeR.constraint_order: The identifiers of constraints in the order they are applied during the filtering procedure. This order is maintained when loading a DesignSettings object.
openPrimeR.relax_order: The identifiers of constraints in the order in which they shall be relaxed during the relaxation procedure when designing primers.
openPrimeR.plot_abbrev: The maximal number of allowed characters for tick labels in plots.
openPrimeR.plot_colors: A named vector providing the identifiers of RColorBrewer palettes. Each vector entry provides the plotting colors for a specific type of stratification (i.e. by run, constraint, or primer). The palettes should provide at least eight colors.