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DNA Fragmentation Instruments and Kits for Next Generation Sequencing

Sample Preparation |  Fragmentation  |  Fragment Size Selection  |  Quality Control  |  Library Preparation  |  Template Enrichtment/ Sequencing

Fragmentation is the process of shredding larger DNA segments or whole genomes into smaller DNA pieces (fragments). DNA fragmentation can be performed by physical methods (nebulization, sonication, column based sharing) or by enzymatically methods based on restriction enzymes. These methods can be adapted in order to obtain the desired fragment size that corresponds to the NGS sequencing read length. 

This website lists different instruments and kits for fragmentation. 

More fragmentation solutions are listed under library preparation kits as some kits include the fragmentation step. 

DNA Fragmentation Instruments

Bioruptor® Pico

The Bioruptor® Pico is the latest innovation in shearing and represents a new breakthrough as an all-in-one shearing system optimized for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml.
Source: diagenode


AFA (Adaptive Focused Acoustics™)

AFA (Adaptive Focused Acoustics™) technology is non-contact and isothermal, providing processing performance and recoveries unmatched by any other sample preparation methodology available today. Covaris Focused-ultrasonicators range from personal use to high-throughput systems including, single-sample, multi-sample, and parallel-processing configurations.
Source: Covaris


EpiSonic™ 2000 Sonication System

The EpiSonic™ 2000 Sonication System is the latest sonication-based instrument with integrated cooling for DNA shearing and chromatin shearing applications. This sonicator is designed for simultaneous, optimized processing of 1 to 12 samples at small microliter-level volumes (optimal at 15 µl of volume), making it an ideal solution for next-generation sequencing due to its high shearing consistency and uniformity.
Source: Epigentek



The Megaruptor® was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA from 2 kb - 75 kb. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly software allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design.
Source: Diagenode


DNA Fragmentation Kits


g-TUBE is a single-use device that shears genomic DNA into selected fragments sizes ranging from 6kb to 20kb. The only equipment needed is a compatible bench-top centrifuge. g-TUBE uses centrifugal force (the “g” in g-TUBE) to push the sample through a precisely manufactured orifice. This produces shearing forces in the sample that fragment the DNA. Fragment size is selected by adjusting the centrifuge rotor speed which alters the flow rate through the orifice and thus the shearing forces. Higher centrifugation RPM will produce shorter fragments and the protocol provided by Covaris contains the settings to generate fragment distributions centered on 6, 8, 10 or 20 kbp.
Source: Covaris


Ion Xpress™ Plus Fragment Library Kit

The Ion Xpress™ Plus Fragment Library Kit provides a rapid and flexible enzymatic-based library construction methodology for the Personal Genome Machine™ sequencing system workflow. Employing enhanced proprietary Ion Shear™ DNA fragmentation chemistry, this revolutionary kit allows completion of library preparation in as little as 2 hours for gDNA and amplicon libraries, removing the need for a physical shearing device to save time and cost.
Source: Thermo Fisher


NEBNext® dsDNA Fragmentase

NEBNext® dsDNA Fragmentase generates dsDNA breaks in a time-dependent manner to yield 50–1,000 bp DNA fragments depending on reaction time (1). NEBNext dsDNA Fragmentase contains two enzymes, one randomly generates nicks on dsDNA and the other recognizes the nicked site and cuts the opposite DNA strand across from the nick, producing dsDNA breaks. The resulting DNA fragments contain short overhangs, 5´-phosphates, and 3´-hydroxyl groups.
Source: NEB


NEXTflex™ AIR Fragmentation Kit

The AIR™ DNA Fragmentation Kit is designed to shear genomic DNA into 150 to 800 bp fragments, which are ideal for second generation sequencing technologies. Nebulization repeatedly forces input DNA through a small hole in the unit, producing random fragments. These fragments are double stranded and contain 3’ overhangs, 5’ overhangs and blunt ends in a heterogeneous mix.