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Old 05-28-2012, 02:42 AM   #1
Junior Member
Location: Cambridge, UK

Join Date: Jun 2011
Posts: 6
Question Primer design software for NGS amplicon sequencing of genes

Hi. I am looking into software packages to design primers for amplifying coding regions of genes. I intend to then sequence these on the Illumina MiSeq/HiSeq. I have been using the Fluidigm platform a lot and they have done a great job designing primers for me. I was wondering though if there are software packages where I can design the primers myself.

There are many packages out there (many based around primer3). The main thing I find hard though is designing primers that tile large exons well using amplicons of appropriate size. The best I have found is ExonPrimer ( This worked very well for me for Sanger sequencing design but doesn’t seem to be that flexible for designing smaller amplicons needed for Illumina NGS.

Does anyone know of any other software that given a list of genes can design primers to produce amplicons (of a specific size range) to tile the coding regions?

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