What Defines A Good Primer Set (In progress)
The goal of this page will be to lay out the current best guesses as to what makes a good primer set. It will also deal with how specific parameters can be tuned to get to a good primer set. This will overlap to a degree with the parameters page (and we will link to the parameters page), but providing it in this format may allow us to reach a broader audience who does not want to read through the whole parameters page.
Using the full foreground genome and full background genome may not always be the best way to design primers, this section will provide recommendations on things to consider when putting together the genome FASTA files.
In an ideal world we would test every possible combination of primers to derive the best primer set. However, the number of possible sets makes this computationally infeasible. This section will provide recommendations on how to get the best primers using swga count and swga filter to more efficiently find selective sets.