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Reader task: a lab member, core-facility user or equipment buyer who has seen “Covaris” or “Bioruptor” on a protocol or quote and needs to know what the instruments do, how they differ, and what to ask before choosing one.
Short answer
Covaris makes focused-ultrasonicators built on Adaptive Focused Acoustics (AFA), a non-contact method that uses controlled bursts of focused high-frequency acoustic energy to fragment DNA and process other samples in a temperature-controlled setting. Bioruptor is a different product line, made by Diagenode, that uses a sonication water bath with a rotating sample holder. Both are used to shear nucleic acids and chromatin; they differ in how the energy reaches the sample.
Definition and scope
“Covaris” is the name of the company and, in lab shorthand, of its instruments. Covaris describes its AFA process as one that “employs highly controlled bursts of focused high-frequency acoustic energy to efficiently and reproducibly process samples in a temperature-controlled and non-contact environment” (Covaris application note M020068). “Non-contact” means no probe is inserted into the sample, which separates AFA from the probe sonicator covered in what a sonicator is.
The most common reason a lab meets these instruments is fragmenting DNA for next-generation sequencing libraries: the same Covaris note states that inefficient fragmentation affects downstream clustering. For where mechanical shearing sits among library-preparation choices, see the NGS library prep kit guide.
This page is general product information. It does not recommend an instrument, and performance statements below are the manufacturers’ own, not independent test results.
How Covaris AFA works
According to the Covaris application note, processing “is accomplished by controlling the creation and collapse of millions of cavitation bubbles within the sample vessel.” The process runs “under isothermal conditions, ensuring the integrity of the nucleic acid sample is maintained and providing high recovery of double stranded DNA.” (For the general physics of cavitation, see how an ultrasonic cleaner works.)
The application note gives one worked example, an amplicon-shearing run on the ME220 focused-ultrasonicator with truSHEAR buffer:
- Sample: 10 µl plus 45 µl of buffer, 55 µl in total.
- Water temperature during the run: 20 °C.
- Readout: fragment size checked on an Agilent Bioanalyzer DNA 12000 chip.
- Targets: amplicons of 2 kb to 400 bp sheared to a 400 to 150 bp range.
These are settings from that one application note and should not be treated as a general protocol; the instrument’s own manual and your library-prep kit’s instructions govern.
Covaris vs Bioruptor-type bath sonicators
Diagenode’s Bioruptor brochure describes Bioruptor Pico and Plus as using “a sonication bath-based rotor”, where “the walls of the sonication bath reflect the ultrasound waves in a random but reproducible pattern”. The sample holder rotates so that tubes receive equal energy, and a water cooler (4 °C) supports isothermal processing. The table puts only documented statements side by side.
| Point | Covaris AFA (application note M020068) | Diagenode Bioruptor Pico / Plus (brochure) |
|---|---|---|
| How energy reaches the sample | Controlled bursts of focused high-frequency acoustic energy; non-contact | Ultrasound reflected within a sonication bath; sample holder rotated through the field |
| Mechanism named | Creation and collapse of cavitation bubbles in the sample vessel | Bath-based sonication (cycles such as 30 s on / 30 s off given as an example) |
| Temperature | Isothermal, temperature-controlled; 20 °C water in the example run | Cooling system with 4 °C water cooler |
| Sample size stated | 55 µl total in the amplicon example | Pico: 5 µl to 2 ml; Plus: 100 µl to 20 ml |
| Samples per run stated | Not stated in the note | Pico: 6 to 12; Plus: 3 to 12 (0.5 to 50 ml sealed tubes) |
| Applications listed | NGS fragmentation (amplicon shearing example) | DNA/RNA shearing, chromatin shearing, FFPE nucleic-acid extraction, tissue and cell disruption, protein/DNA/RNA extraction |
The Bioruptor brochure also lists other Diagenode devices: Diagenode One (desktop, 20 or 50 µl microfluidic chips, NGS DNA shearing) and Megaruptor (automated, 2 to 75 kb long-fragment DNA shearing). The brochure is a dated vendor document, so confirm current models and specifications with the maker.
What is a Bioruptor?
A Bioruptor is a Diagenode bath sonicator. Samples in sealed tubes sit in a rotating holder in a cooled water bath and are exposed to repeated on/off sonication cycles. The brochure lists chromatin shearing (for example before ChIP, see ChIP-seq) and cell or tissue disruption before mass spectrometry among its uses.
Where it matters for lab decisions
These questions follow directly from the differences documented above; they are a checklist for reading vendor documents, not a ranking.
- Sample volume and vessel: what range does the maker state, and does it fit your input (a few microlitres of amplicon, or millilitres of cell lysate)?
- Throughput: how many samples per run are stated for the model you are considering?
- Temperature control: is the cooling or isothermal claim part of the maker’s specification for your application, and at what stated temperature?
- Readout: how will you check fragment size (the Covaris example uses a Bioanalyzer chip)? Whichever instrument you use, size distribution is confirmed afterwards, not assumed.
- Consumables and protocol fit: which tubes, vessels or buffers does the method you are following specify?
- Access: many labs reach these instruments through a core facility; see core facility staff authorship for how sequencing-core work is credited.
Common misunderstandings
- “Covaris” and “Bioruptor” are not the same technology. They are different makers using different delivery of ultrasound, per each maker’s own documents.
- “Non-contact” does not mean “no cavitation”. The Covaris note says the process works through cavitation bubbles inside the sample vessel.
- Vendor claims are not comparisons. The documents cited here are manufacturers’ descriptions; neither compares itself with the other.
- One application note is not a universal setting. Times, power and buffer depend on the sample type and target size.
FAQ
What does Covaris AFA stand for?
Adaptive Focused Acoustics, Covaris’s term for its non-contact method of delivering focused acoustic energy to a sample.
Is a Bioruptor a Covaris product?
No. In the brochure cited here, Bioruptor is a Diagenode product line.
What are these instruments used for?
Per the documents cited: fragmenting DNA for sequencing libraries, shearing chromatin and RNA, and disrupting cells or tissue for extraction.
Sources
- Covaris, application note “Amplicon Shearing Using a Covaris Focused-ultrasonicator” (M020068), PDF: https://cdn.shopify.com/s/files/1/0377/2163/6908/files/M020068.pdf, read 2026-11-08.
- Diagenode, Bioruptor sonicator brochure, PDF: https://mhir.org/wp-content/uploads/2017/01/Bioruptor_Sonicator_Brochure.pdf, read 2026-11-08 (vendor document; model range may have changed).
