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. A 12 sample cassette is also available for purchase separately for increased throughput. 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.

Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.


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

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    Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.
    Park Do-Young et al.
    The 3.0-Mb complete genome of Lacticaseibacillus rhamnosus strain DM065, which was isolated from the oral cavity of healthy volunteers in South Korea, was sequenced using a combination of PacBio and Illumina technologies. The genome consists of one circular chromosome and two plasmids and lacks antimicrobial resista...

    Semi-automated assembly of high-quality diploid human reference genomes.
    Jarvis Erich D et al.
    The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telom...

    Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.
    Schöpflin R.et al.
    Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read ge...

    The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)
    Ebdon S. et al.
    We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74\%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assemble...

    The genome sequence of the satellite, Eupsilia transversa (Hufnagel,1766)
    Crowley L. et al.
    We present a genome assembly from an individual female Eupsilia transversa (the satellite; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 467 megabases in span. The entire assembly (100\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete...

    The genome sequence of the common yellow swallowtail, Papilio machaon(Linnaeus, 1758)
    Lohse K. et al.
    We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosom...

    The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)
    Lohse K. et al.
    We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mit...

    Complete Genome Sequence of Strain DM083 Isolated from HumanTongue Coating.
    Park Do-Young et al.
    We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Importantly, the genome is devoid of the antimicrobial resistance gene, sa...

    The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)
    Boyes Douglas and Lees David
    We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100\% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The compl...

    The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)
    Boyes Douglas and Boyes Clare
    We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete ...

    The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)
    Boyes Douglas and Gibbs Melanie
    We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The ...

    Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.
    de Abreu Vinicius A C et al.
    Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and compara...

    The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity
    Fan Li et al.
    Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the worldwide famous cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with...

    The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.
    Berasategui Aileen et al.
    Many insects rely on microbial protection in the early stages of their development. However, in contrast to symbiont-mediated defense of eggs and young instars, the role of microbes in safeguarding pupae remains relatively unexplored, despite the susceptibility of the immobile stage to antagonistic challenges. Here,...

    The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)
    Crowley Liam M. and Mulley John
    We present a genome assembly from an individual male Acanthosoma haemorrhoidale (hawthorn shieldbug; Arthropoda; Insecta; Hemiptera; Acanthosomatidae). The genome sequence is 866 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 7 chromosomal pseudomolecules with the X and Y sex chromosome...

    The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)
    Boyes Douglas et al.
    We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mit...

    Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing
    Yang X. et al.
    The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (...

    The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900
    Macadam Craig et al.
    We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was foun...

    The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)
    Falk Steven and Monks Joseph
    We present a genome assembly from an individual male Lasioglossum lativentre (the furry-claspered furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. The majority of the assembly (75.22\%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome...

    Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map
    Smolander Olli-Pekka et al.
    Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map...

    The genome sequence of a parasitoid wasp, Forster, 1771.
    Broad Gavin
    We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein c...

    Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).
    Huang Yi et al.
    Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essenti...

    Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.
    Fang Li Tai et al.
    The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived...

    De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).
    Pickett, Brandon D and Glass, Jessica R and Ridge, PerryG and Kauwe, John S K
    The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale ...

    Targeted long-read sequencing identifies missing disease-causingvariation.
    Miller Danny E et al.
    Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully expl...

    Evidence of an epidemic spread of KPC-producing in Czech hospitals
    Kraftova Lucie et al.
    The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018–2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the pr...

    Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.
    Wahlster, Lara and Verboon, Jeffrey M and Ludwig, Leif S and Black, Susan Cand Luo, Wendy and Garg, Kopal and Voit, Richard A and Collins, Ryan L andGarimella, Kiran and Costello, Maura and Chao, Katherine R and Goodrich,Julia K and DiTroia, Stephanie
    Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleot...

    PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.
    Artesi, M. et al.
    The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral inse...

    Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.
    Formenti G. et al.
    BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for sim...

    Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.
    Tvedte, Eric S and Gasser, Mark and Sparklin, Benjamin C and Michalski,Jane and Hjelmen, Carl E and Johnston, J Spencer and Zhao, Xuechu andBromley, Robin and Tallon, Luke J and Sadzewicz, Lisa and Rasko, David Aand Hotopp, Julie C Dunning
    The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throug...

    A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.
    Liu H. et al.
    Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population result...

    Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).
    Xia Z. et al.
    Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. T...

    Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.
    Suzuki Y. et al.
    Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations i...

    Efficient hybrid de novo assembly of human genomes with WENGAN.
    Di Genova A. et al.
    Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very hi...

    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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