DNA/RNA Shearing for NGS

Nucleic acid fragmentation is a crucial first step in the Next-Gen Sequencing workflow. While there are a variety of methods available, mechanical DNA shearing powered by AFA-energetics® remains the method of choice for achieving high sensitivity and unbiased results.

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AFA Process for DNA and RNA Shearing

Adaptive Focused Acoustics® (AFA®) technology is firmly established as the fragmentation method of choice for NGS, and Covaris continues to innovate the tools required to shear DNA and RNA without GC bias or thermal damage.
The Covaris AFA process is conducted under isothermal conditions, ensuring the integrity of the nucleic acid sample is maintained and providing high recovery of double-stranded DNA during the shearing process.
Combined with the specifically engineered AFA Tubes, it is possible to precisely and accurately fragment DNA and RNA to the 100 – 1500bp range (microTUBE). Focused-ultrasonicators range from low to high throughput, including automation-friendly options.

Benefits of AFA Technology for DNA and RNA Shearing

Physical shearing of DNA or RNA using Covaris AFA is concentration independent, isothermal, and highly reproducible. Physical shearing does not require a cleanup step after shearing, thereby preserving the complexity of the sample for library preparation. This shearing method provides unmatched control and reproducibility of shearing.
Temperature ControlledProcessing at controlled temperatures provides highest yields while preserving sample fidelity
Accurate and preciseHighly reproducible process, day to day, user to user. Protocols can be transferred instrument to instrument without further optimization
Non-contact, closed vesselNo cross-contamination, clean-up, or sample loss
VersatileGenerate tight fragment distribution centered from 100 bp to 20 kbp
DNA Shearing of Clinical Samples

Unparalleled acoustic energy control enables shearing across a wide range of fragment sizes, ranging from 150 bp to 5 kb. AFA-energetics is the gold standard for DNA shearing, providing you with highest sample complexity and unbiased sample yield to pave the way for the most cost-effective library prep.
RNA Shearing

Total RNA sheared with Covaris AFA from FFPE samples. These electropherograms show unbiased RNA fragment size distribution.

Total mRNA Shearing

Agilent BioAnalyzer electropherogram of 5 µg of mRNA processed in a volume of 130 µl of TE in a microTUBE according to the operating conditions, showing the mean fragment size at 200 bases.

Comparison of Shearing Fragment Sizes

Fragment Size*Sample VolumeCovaris Products
175 to 1.5 kbp5 to 50 µlAFA-TUBE
150 to 1.5 kbp130 µlmicroTUBE-130
150 to 1.5 kbp55 µlmicroTUBE-50
150 to 1.5 kbp15 µlmicroTUBE-15
6 – 20 kb150 µlg-TUBE
*For validated fragment sizes, refer to the Covaris Focused-ultrasonicator DNA and RNA Shearing Protocols.



A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Fisher et al. Genome Biology 2011
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Aird et al. Genome Biology 2011
Solution-based targeted genomic enrichment for precious DNA samples. Shearer, AE et al. BMC Biotech 2012