Figure 1: Schematic of the design strategy and workflow for ThermoAlign.
From: ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
A single run parameters file is used by all components of the pipeline. Colored boxes represent the four core modules of ThermoAlign, enumerated in their order of operation: (1) target region selection, (2) unique oligonucleotide design, (3) primer specificity evaluation, and (4) primer pair selection. Dashed boxes represent sub-routines within each of these modules and arrows depict their order of operation. The remaining elements are the database (reference genome sequence), external files (variant call format [.vcf] files and a run parameters file) and functions (nearest-neighbor model for the Tm of homodimer, heterodimer and hairpin interaction functions in Primer3). Connecting lines for these remaining components depict dependencies for the connected components (a filled dot is used to indicate the source from which information or a function is pulled). Required inputs for ThermoAlign are indicated by an asterisk.
