Primer Design for Targeted Deep Sequencing

Validated Pipeline for Primer Design and in-silico PCR

DNA double helix with ACGT and binary numbers in the background.


Submit positions to

v0 Primer Design Pipeline (first generation)

v1 Primer Design Pipeline

v2 Primer Design Pipeline (input your own sequence with SNPs)



Open-sourced and published tools for generating and in silico testing of primers designed for deep sequencing (validation) of single nucleotide positions on the Illumina MiSeq Sequencer.

The workflow that this primer design pipeline automates is part of our current SOP and is currently in routine laboratory use (see publications in references).

Please familiarize yourself with the workflow before submission to the Pipeline.

For the various primer3 settings used in the pipeline, please see here.

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