Megaruptor® 3

Tight fragment size distribution
High quality libraires
1 to 8 samples in parallel
Tuneable to between 5 - 100 kb
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1 unit

The Megaruptor® 3 was designed to provide the best experience with the fragmentation of DNA from 5 kb - 100 kb. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for 8 samples to be processed simultaneously without additional user input. Just set the desired parameters and the automated system takes care of the rest. The shearing with the Megaruptor leads to optimal long-read sequencing using PacBio®'s, and Oxford Nanopore™ technologies' systems.


As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.

Brewster Kingham, Delaware Biotechnology Institute, University of Delaware

The NGS Competence Center Tübingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.

Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.

Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/µL and up to 70 ng/µL, saving sample material for optimization and meeting downstream requirements for library preparation.  

Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.

Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen
  • Demonstrated shearing of DNA from 5 -100 kb

    Excellent reproducibility and size distribution achieved with the Megaruptor 3

    A: Fragment Analyzer profiles of human genomic DNA samples (25 ng/μl; 200 μl/sample) sheared to 6, 10 and 30 kb. B: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)

  • Specifications for the Megaruptor
    Megaruptor 3Megaruptor 3 Megaruptor 2Megaruptor 2
    Size range 5 - 100 kb 3 - 75 kb
    Volume range 65 - 500 µl 50 - 400 µl
    Concentration range 0 - 150 ng/µl 0 - 50 ng/µl
    Throughput 1 to 8 samples in parallel 1 to 2 samples in series
    Eliminate cross-contamination with disposable elements in a completely closed-system with disposable elements and with washing sequences
    Multiple-orifice disposables
    Consumables Megaruptor 3 Shearing Kit : 
    Cat. No. E07010003

    Hydropore - short : Cat. No. E07010001
    Hydropore - long : Cat. No. E07010002
    Hydro Tubes : Cat. No. C30010018

  •  Testimonials

    The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.

    Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.
  • Video
  •  Documents
    Megaruptor® 3 FLYER
    Your partner in long-read sequencing Designed to provide simple and automated DNA sample prepara...
    Megaruptor 3® Manual MANUAL
    Megaruptor 3 Manual - DNA Shearing System The Megaruptor 3 was designed to provide researchers w...
    Megaruptor® 3 Quick guide QUICK GUIDE
    The Megaruptor® 3 is intended for laboratory use. It is not suitable for clinical use. Use of...
  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: Megaruptor® 3 (Diagenode Cat# B06010003). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Complete Genome Sequence of sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.
    Chéraiti, Nardjess and Plewniak, Frédéric and Tighidet, Salima andSayeh, Amalia and Gil, Lisa and Malherbe, Ludivine and Memmi, Yosr andZilliox, Laurence and Vandecasteele, Céline and Boyer, Pierre andLopez-Roques, Céline and Jaulhac, Benoît and Bensou
    sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and on...

    Contrasting signatures of genomic divergence during sympatric speciation.
    Kautt, Andreas F and Kratochwil, Claudius F and Nater, Alexander andMachado-Schiaffino, Gonzalo and Olave, Melisa and Henning, Frederico andTorres-Dowdall, Julián and Härer, Andreas and Hulsey, C Darrin andFranchini, Paolo and Pippel, Martin and Myers,
    The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark...

    Genome structure and content of the rice root-knot nematode ().
    Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B
    Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this s...

    Repeat expansions confer WRN dependence in microsatellite-unstablecancers.
    van Wietmarschen, Niek and Sridharan, Sriram and Nathan, William J andTubbs, Anthony and Chan, Edmond M and Callen, Elsa and Wu, Wei and Belinky,Frida and Tripathi, Veenu and Wong, Nancy and Foster, Kyla and Noorbakhsh,Javad and Garimella, Kiran and Cr
    The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However...

    Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.
    Zhao, Hu and Chen, Yuan and Shen, Chanjuan and Li, Lingshu and Li, Qingzhaoand Tan, Kui and Huang, Huang and Hu, Guoyu
    BACKGROUND: The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHOD...

    Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.
    Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F
    Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This var...

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