Illumina DNA PCR-Free

Method for shotgun DNA libraries used for whole genome sequencing and metagenomics.

Illumina’s new tagmentation-based DNA PCR-free library preparation is the method of choice for generating the highest quality DNA sequencing libraries. PCR-free libraries have better coverage of GC-rich regions compared to PCR-based methods and the reads are more evenly distributed over the genome.

This method is recommended when:

  • You want a fast protocol that can be used for a wide range of input amounts.
  • Insert sizes approx. 350 bp are suitable for your application.
  • You do not have enough DNA for the TruSeq PCR-free protocol

Sample requirements

  • Sample type: DNA
  • Volume: >30 µL (max 100 µL per well)
  • Amount of material needed for 1 library preparation: 25-2000 ng, depending on sample type
    • For larger genomes (> 1Mb) min 300 ng
    • For smaller (eg bacterial) genomes min 100 ng
    • A low input protocol is available for samples with < 100 ng, please ask our project coordinators for further info
  • Concentration: min 5-15 ng/µL, depending on sample type and genome size, please ask our project coordinators for further info

How to evaluate the sample quality

We check your samples upon arrival, however we still require our users to do their own QC steps before sending samples.

Checking the concentration
Please use fluorometric measurements (e.g. Qubit, Quant-it), not absorbance measurements (Nanodrop, spectrophotometer).

Checking the quality and purity
The DNA should be in EB buffer (not EDTA or water), of high quality, and ideally have an OD260/280 of 1.8-2.

If your samples are below the required thresholds, please get in touch.

What we do with your samples

Once your samples arrive at NGI, we start by performing a reception control step in which we make sure the samples meet our requirements.

If the samples fail this quality control step, we will contact you to discuss possible options. Should you choose to proceed with samples not fulfilling the criteria it will be at your own risk, NGI will only make one attempt at library preparation and if the prep does not work you will have to pay for the library preparation anyway.

If the samples pass reception control, we will inform you and the samples will be queued for library preparation.

Library preparation

Library QC and sequencing

We evaluate the concentration of the library and inform you of the QC status of each sample. Once the libraries have passed this QC step, they are normalised, pooled, and queued for sequencing.

The sequencing will be carried out following the setup stated in the agreement.

Expected results

PCR-free libraries are well suited for deep sequencing to achieve high coverage genomes. The library preparation method shows a significantly better coverage of GC-rich regions compared to PCR-based methods and the reads are more evenly distributed over the genome.

Relevant Technologies
Bioinformatics Pipelines
Method Status


We are currently testing this method. Please contact us to find out more.