Amplicon-seq is an easy and inexpensive method for preparing focused NGS libraries from gDNA. Amplicon-seq utilizes a first PCR process to generate the amplicon that will be the focus of the sequencing and a second PCR process to attach barcodes required for the NGS.

For samples addressing 1 or 2 PCR products, the first step PCR can be performed in your lab or at Syntezza. Larger amplicon pools are developed by our staff and the PCR performed at Syntezza.

The second step PCR is performed at Syntezza, prior to the NGS sequencing. When sequencing is competed, we can also facilitating bioinformatic analysis of the results.


SKU: N/A Category:
Image Variation SKU Price Quantity Add To Cart
Extraction 1 24 Samples - A-S Extract 1-24 40.00
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Extraction 25 48 Samples - A-S Extract 25-48 35.00
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Extraction 49 96 Samples - A-S Extract 49-96 30.00
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Extraction > 96 Samples - A-S Extract 96+ 25.00
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Both PCR Prep Steps 1 24 Samples - A-S Full Prep 1-24 86.00
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Both PCR Prep Steps 25 48 Samples - A-S Full Prep 24-48 80.00
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Both PCR Prep Steps 49 96 Samples - A-S Full Prep 49-96 75.00
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Both PCR Prep Steps >96 Samples - A-S Full Prep 96+ 70.00
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Barcoding Prep Only 1 24 Samples - A-S Barcode Prep 1-24 54.00
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Barcoding Prep Only 25 48 Samples - A-S Barcode Prep 25-48 48.00
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Barcoding Prep Only 49 96 Samples - A-S Barcode Prep 49-96 43.00
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Barcoding Prep Only >96 Samples - A-S Barcode Prep 96+ 40.00
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Sequencing 2x150bp 100K Reads - A-S Sequencing 2x150bp 100K 67.00
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Sequencing 2x150bp 25M Reads - A-S Sequencing 2x150bp 25M 10,989.00
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Sequencing 2x250bp 100K Reads - A-S Sequencing 2x250bp 100K 91.00
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Sequencing 2x300bp 100K Reads - A-S Sequencing 2x300bp 100K 102.00
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Ship GenTegra - A-S Ship 12.00
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gDNA extraction

Prior to preparing the amplicon library, we can pick up your  samples and perform the DNA  extraction at our facility or you can isolate the gDNA at your lab. DNA extraction service is available from ₪25.00 to ₪40.00 per sample.

Preparation of the amplicon library

The first step PCR reaction utilizes custom PCR primers designed to amplify your specific region of interest plus an additional 20 bp region upstream of each primer, called Linkers.

The linker sequence for the forward primer is CS1: 5’-ACACTGACGACATGGTTCTACA-[locus specific sequence – Forward primer].

The linker sequence for your reverse primer is CS2: 5’-TACGGTAGCAGAGACTTGGTCT-[locus specific sequence – Reverse Primer]

You can order the primers from IDT and perform the first stage PCR at your lab and simply send us the PCR product amplicons. We will then perform the second step PCR that adds a barcode to each sample to finalize your library in preparation for NGS sequencing. Pricing for this second step PCR is available from ₪40 to ₪54 per sample.

Alternatively, you can email your custom primer sequences to Syntezza. We will order the primers with the added linker sequences and perform the first step PCR as well as the second step PCR to finalize your library in preparation for NGS sequencing. Price for the complete Amplicon-Seq library preparation from gDNA is available for the cost of the custom primers plus ₪70 to ₪86 per sample.

The above processes are effective for NGS sequencing of at most a few PCR product targets in each sample well.

For larger pools of PCR product amplicons, use RhAmp-Seq

An alternative system is required for larger pools to mitigate primer-dimer formation and proliferation of off-target PCR reactions. IDT’s RhAmp-Seq system is a  cost effective method that enables highly accurate NGS amplicon sequencing for up to thousands of targets. The fast and easy RhAmp-Seq workflow, based on IDT’s proprietary RNase H2-dependent PCR (rhAmp PCR) technology, generates NGS-ready amplicon libraries for deep, targeted resequencing. To learn more about IDT’s RhAmp-Seq technology, visit this page.

Syntezza’s scientific support staff can help you design your unique RhAmp-Seq primer set and prepare a custom price quotation. When the project is approved, we will pick up your samples or gDNA, obtain the reagents from IDT and perform the library preparation.


GenTegra technology enables shipping of DNA samples at ambient temperature without any fear of degradation, sample loss or delay in transport. Syntezza will deliver to your lab the appropriate number of GenTegra tubes required to stabilize your samples for transport to our facilities in Jerusalem and will use GenTegra tubes to safely transport your prepared libraries to the NGS sequencing facility. Shipping with GenTegra tubes is provided at ₪12 per sample.

NGS sequencing

For Amplicon-seq libraries, we offer four sequencing options using Illumina MiniSeq or MiSeq instruments.

Number of Reads Read Size  Price
100,000 2 x 150 bp ₪ 67
25 million 2 x 150 bp ₪ 10,989
100,000 2 x 250 bp ₪ 91
100,000 2 x 300 bp ₪ 102

Our NGS specialists will help you select the best options and prepare a custom price quotation. Contact us today at or call 02-586-7138 ext. 2.

Additional information


Extraction 1-24 samples, Extraction 25-48 samples, Extraction 49-96 samples, Extraction > 96 samples, Both PCR Prep Steps 1-24 Samples, Both PCR Prep Steps 25-48 Samples, Both PCR Prep Steps 49-96 Samples, Both PCR Prep Steps >96 Samples, Barcoding Prep Only 1-24 Samples, Barcoding Prep Only 25-48 Samples, Barcoding Prep Only 49-96 Samples, Barcoding Prep Only >96 Samples, Sequencing
2x150bp 100K reads, Sequencing 2x150bp 25M reads, Sequencing 2x250bp 100K reads, Sequencing 2x300bp 100K reads, Ship GenTegra

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