Next Generation Sequencing

DNA Shearing, library preparation, and automation: your one-stop shop for NGS

1. Choose your shearing device: Shear DNA anywhere from 150 bp to 75 kb

Shear down to 5 μl: 150 bp - 2 kb
Perfect for NGS DNA library prep and FFPE nucleic acid extraction
Shear anywhere from 2 kb – 75 kb
Perfect for mate pair library prep and long fragment DNA sequencing
Shear 20 or 50 µl with this light desktop device

2. Choose your optimized library preparation kit

3. Choose library prep automation for unmatched data reproducibility

Low input of 50 pg: MicroPlex Library Preparation Input above 5 ng: iDeal Library Preparation Achieve great NGS data easily
Why Diagenode is the right provider for your NGS needs?

Diagenode has specialized in epigenetics studies for over 15 years. We first developed a unique shearing system for chromatin for ChIP studies. Our expertise easily lent itself to state-of-the art shearing devices for DNA, now down to shearing volumes of 5 ul, perfect for NGS DNA library preparation. We have since developed industry-leading kits for ChIP-seq, Methyl-seq, and NGS library preparation. We also offer a unique automation system that automates and perfects libray prep as well as immunoprecipitation studies. It’s a perfect combination!

  • Trusted shearing devices
  • Library preparation kits for a range of inputs
  • Unique automation device
  • Understanding Next Generation Sequencing

    Next-generation sequencing (NGS) empowers sequencing with remarkable throughput and scale and generates hundreds of billions of bases per day. The high-throughput aspect of NGS lowers the cost of sequencing while delivering rapid, accurate and reproducible data sets, which opens the door to new research areas. NGS refers to genome sequencing, genome resequencing, de novo sequencing, transcriptome sequencing, detecting DNA-protein interactions, and epigenome characterization to name a few. Demand for exponentially increasing sequencing data meets challenges such as computational analysis bottlenecks, interpretation and data storage.

    Depending on the application and starting material there are currently several commercialized NGS platforms available that use distinct chemistries to allow massively parallel sequencing of many millions to billions of template DNA molecules. For several NGS platforms material requires prior construction and library preparation.

    There are also significant challenges for NGS – in particular data processing and analyses. It is worth to keep in mind that not discussed here, the third-generation technologies may further revolutionize genomics research!

    NGS Applications:

    • Whole genome sequencing
    • De novo sequencing
    • Targeted sequencing
    • Exome sequencing
    • Transcriptome sequencing
    • Genome sequencing
    • Mitochondrial sequencing
    • DNA-protein interactions (ChIP-seq)
    • Variant detection
    • Genome finishing

    NGS in Research Areas:

    • Oncology
    • Reproductive health
    • Forensic genomics
    • Agrigenomics
    • Complex diseases
    • Microbial genomics
    • Food and environmental genomics
    • Genomics in drug development – personalized medicine

    Terminology in NGS

    a single contiguous stretch of sequence obtained from the instrument
    Fragment read
    a read from a fragment library. Depending on the sequencing platform, a read is typically around 100-300bp
    Fragment paired-end reads
    two reads from each end of a DNA fragment coming from a fragment library
    Mate-paired read
    two reads from each end of a large DNA fragment (usually a pre-defined size-range)
    Coverage (example)
    30× coverage means that each base pair in the reference genome was covered by 30 reads on average

    NGS platforms


    Illumina uses a sequence-by-synthesis technology with fluorescently labelled reversible chain terminator nucleotides, which are situated on clonally amplified DNA templates (clusters). DNA clusters are immobilized on a surface of a glass flowcell. The workflow composes of repeated cycles: incorporation of all four nucleotides (each with labelled with different fluorescent dye), four-color imaging, cleavage of dye and terminating groups, and again incorporation, imaging etc. The flowcells are subjected to massively parallel sequencing. This strategy possibly avoids errors with mononucleotide runs by controlled addition of a single fluorescently labelled nucleotide at a time. Read lengths are usually around 100-150 bp.

    Ion Torrent

    Ion Torrent is powered by semiconductor technology chips and detects the protons released upon incorporation of nucleotides during synthesis. It uses emulsion PCR (emPCR) on the surface of beads called Ion Sphere Particles and amplifies DNA fragments with linked specific adapters. Each bead is covered by one-type DNA fragment. Beads with different DNA fragments are then located in a proton sensing wells of a chip. Chip is flooded with one of the four nucleotides at a time, and the process is repeated every 15 seconds with the different nucleotide. So during sequencing each of the four bases is introduced one by one and in an event of incorporation, protons are released, and a voltage signal is detected proportionally to the incorporation.

    Pacific Biosciences

    Pacific Biosciences enables observing of structural and cell type variation by single molecule real time (SMRT) sequencing with ultra-long read lengths of >20kb base pairs. In this platform ultra-long double stranded DNA (dsDNA) fragments are generated either by random shearing with Diagenode device such as the Megaruptor® or by amplification of target regions of interest. A SMRTbell library is generated by ligating universal hairpin adapters to each end of DNA fragments. After washing steps with size selective conditions, sequencing primers are annealed to the SMRTbell templates and sequencing, involving a DNA polymerase bound to a DNA template, begins in the presence of fluorescently labelled nucleotides. When each base is incorporated, a different pulse of fluorescence is detected in real time.

    Oxford Nanopore

    Oxford Nanopore develops a technology, based on a single DNA molecule sequencing, where a biological molecule, i.e. DNA passes through or near nanoscale pores (nanopores) located as a set of electically resistant polymer membrane, and changes an ionic current. The information on this change is translated into information of the molecule for example by distinguishing all four nucleotides (A or G r C or T) as well as modified ones. A flow cell of the sequencing minION device contains a sensor array of several hundred nanopore channels. The DNA sample requires ultra-long DNA fragments that can be generated by randon shearing with Diagenode device such as the Megaruptor®.


    SOLiD, with a unique chemistry, enables simultaneous sequencing of thousands of individual DNA molecules. It starts with library generation by ligation of adapters to sheared genomic DNA (fragments of mate-pair libraries are suitable). In the next step, the emulsion PCR (emPCR) is carried out to amplify individual template DNA molecules clonally on the surface of a bead. In emPCR, individual DNA templates are mixed with PCR reagents and a primer-coated beads within an aqueous droplet surrounded by a hydrophobic shell within an oil-in-water emulsion are randomly attached to the surface of a glass slide that is loaded for sequencing on the instrument. This technology uses a set of four fluorescently labelled di-base probes that compete for ligation to the sequencing primer


    454 utilizes a large-scale parallel pyrosequencing. It starts with library preparation on 300-800 bp fragments of either the whole genome DNA or targeted gene fragments. The next step involves attachment of adapters to the DNA fragments and separation into single DNA strands. Later on adapter ligated DNA fragments are processed in emulsion-based clonal amplification (emPCR) and the DNA library fragments are located onto micron-sized beads. Each DNA-bound bead is placed into a well on a fiber optic chip and inserted into the instrument. The four DNA nucleotides are added sequentially in a fixed order during a sequencing run and sequenced in parallel.

  • DNA/RNA library preparation

    Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to fragmented DNA or RNA prior to sequencing After in...
  • DNA/RNA shearing

    In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniqu...
  • FFPE DNA extraction

    Diagenode's high yields FFPE DNA extraction using Bioruptor® is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction k...
  • RNA extraction

    Various biochemical and analytical techniques require the extraction of RNA from tissues. Isolating intact RNA is essential for many techniques used in gen...

Made for Next Generation Sequencing

Cat. No.ProductFormatPrice
B01070001 Diagenode One sonication device
The Diagenode One is the new desktop solution that provides optimal DNA shearing for Next-Generation-Sequencing and Chromatin shearing for ChIP...
1 unit
C05010020 iDeal Library Preparation Kit x24 (incl. Index Primer Set 1)
The iDeal Library Preparation Kit reliably converts DNA into indexed libraries for next-generation sequencing, with input amounts down to 1 ng. Our kit offer...
24 rxns $890.00
B03000002 IP-Star® Compact Automated System
The IP-Star® Compact Automated System provides the flexibility needed to change multiple parameters in the protocols to achieve optimal experimental cond...
1 unit
B06010002 Megaruptor® 2
The Megaruptor® 2 was designed to provide the best experience with the fragmentation of DNA from 3 kb - 75 kb. Shearing performance is independent o...
1 unit
C05010012 MicroPlex Library Preparation Kit v2 (12 indices)
Specifically optimized for ChIP-seqThe MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allow...
12 rxns $1,100.00
B01060001 Bioruptor® Pico sonication device
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-...
1 unit
B06010001 Megaruptor®
The Megaruptor® was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA from 2 kb - ...
1 unit
C05010014 MicroPlex Library Preparation Kit v2 (48 indices)
Specifically optimized for ChIP-seqThe MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allow...
48 rxns $4,300.00


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