NGS-PrimerPlex v1.3.0

Several important improvements were made:

• Now users can add uridines into primers! Two parameters control their location: -umaxtm (the maximal acceptable Tm for Tm of primer parts left after primer cleavage by uridine) and -unucs (number of nucleotides from 3'-end of primer in which one T should be replaced with U. The 2nd U is inserted in the left part of primer in such a way that Tm for two parts is maximally equal. By default, T is not replaced with U at all)
• Users can skip bad primers that do not correspond to new parameters, and new versions will be designed for them!
• Non target amplicons are written to 2nd worksheet in the all_internal_primers_specificity.xls file.
• Primers that form very stable dimers (controlled by the -minmultdimerdg2 argument) are not allowed even in different multiplexes!
• Primers that can be joined into one block are saved into new type of draft primers - all_draft_primers_after_joinment.xls. Primers that are thought to prevent this joinment are excluded.
• Some bugs were fixed.