Genomics & Bioinformatics Core Facility

Covaris Fragmentation

Illumina recommends the Covaris focused-ultrasonicator system to fragment DNA in preparation of DNA sequencing libraries. Ultrasonication is favored over other fragmentation methods because DNA molecules are randomly broken with minimal bias. Ultrasonication avoids the limitation observed with Nebulization and enzymatic methods. The Genomics Core facility provides DNA fragmentation services using the Covaris S220 Ultrasonicator System. Nucleic acid fragmentation is applicable to many applications including chromatin shearing, tissue homogenization, cell lysis, compound dissolution, and particle micronization. For custom services, contact us.

Fragmentation Parameters

DNA fragmentation with the S220 produces consistent, reproducible results. To achieve the desired average size distribution, refer to the table to choose the appropriate Adaptive Focused Acoustics (AFA) tubes. See the Covaris DNA Shearing Guide for more information.

Covaris AFA Tubes
Range of Fragment Size Distribution
Volume of Sample Required
150bp – 1,500bp
150bp – 1,500bp
2- 5kb
6 – 20kb

Sample Preparation

To ensure successful results, the sample must be of sufficient purity and appropriate concentration. We recommend using only purified products. Quality of the sample is very important for accurate fragmentation; high salt concentration and particulates are known to adversely affect results. 

Selecting the appropriate fragmentation parameters is sample concentration dependent. So it is important to determine sample concentration prior to submission. We recommend using a spectrometer, such as the Nanodrop.

For each sample to be processed, provide 100ng to 5ug of your sample in clearly labeled 1.5ml tubes. All tubes must be labeled on the side with PI Name, Date (MM/DD/YYYY), Concentration, and unique Sample Name. We strongly recommend providing an aliquot for processing; do not send the primary stock. Dilutions should be made using Tris-EDTA, pH 8.0 buffer. Do not exceed a final volume of 50ul.

Please follow all instructions as detailed in the Sample Preparation Guidelines. To avoid sample-processing delays, ensure your tubes/plates are clearly labeled with your initials, date, and sample number.

Contact us to schedule delivery of your samples to our Genomics Core Facility.

Genomics Core Facility
Galvin Life Science Center Room 019
Phone: (574) 631-1902


After service completion, the fragmented sample is returned in a sterile 1.7mL microcentrifuge tube and documentation of parameters is provided. For an additional fee, we can assess the size distribution using the Agilent 2100 Bioanalyzer and the sample concentration by Qubit Quantification. For addtional services, contact us.