sparQ DNA Frag & Library Prep Kit

Integrated enzymatic fragmentation and library prep with unrivaled speed and performance

Features & Benefits

  • High quality libraries in 2.5 hours from 1 ng – 1 μg of input DNA
  • Tunable and reproducible fragmentation size range
  • Simple, convenient 2-step workflow with minimal hands-on time
  • Novel chemistry and high-fidelity amplification minimizing bias
  • Superior sequence coverage uniformity and low duplication rate

 

sparQ DNA Frag & Library Prep Kit is intended for molecular biology applications. This product is not intended for the diagnosis, prevention or treatment of a disease.

Description

The sparQ DNA Frag & Library Prep Kit is optimized for enzymatic fragmentation of DNA and streamlined construction of high quality libraries for sequencing on Illumina NGS® platforms. The simple, convenient 2-step workflow can be completed in 2.5 hours with minimal hands-on time and accommodates DNA input amounts from 1 ng to 1000 ng. The DNA fragmentation and polishing reactions are combined in a single step to generate 5'-phosphorylated and 3'-dA-tailed fragments. This is followed by high efficiency adapter ligation in the same tube. PCR-Free workflows are enabled from 100 ng of starting material. If library amplification is required, the HiFi PCR Master Mix and Primer Mix ensure even amplification with minimal bias.

 

Streamlined  workflow

sparQ DNA Frag & Library Prep workflow


sparQ DNA Frag & Library Prep workflow

The streamlined workflow utilizes a proprietary enzyme mix that combines fragmentation and DNA polishing in a single step to simplify library construction. High efficiency adapter ligation and cleanup are performed in the same tube, followed by an optional amplification step using HiFi PCR Master Mix and Primer Mix.


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  • Generates high quality libraries in 2.5 hours with minimal hands-on time
  • Simplified 2-step workflow minimizes sample loss


Tunable & reproducible fragmentation

Fragmentation time course


Fragmentation time course

sparQ DNA Frag & Library Prep Kit is tunable to the desired fragment size. 100 ng Human gDNA was subjected to fragmentation with a series of incubation time points (3 – 18 min). After fragmentation, DNA samples were purified and then visualized using Agilent High Sensitivity DNA Kit.


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  • Fragmentation profile closely resembles Covaris mechanical shearing
  • Proprietary frag and polishing enzyme mix ensures tunable and reproducible fragmentation across a wide range of DNA input


High coverage uniformity

Genome coverage analysis


Genome coverage analysis

Library prepared using sparQ DNA Frag & Library Prep Kit resulted in uniform coverage across a wide range of GC-content. Libraries were prepared using different DNA fragmentation and library preparation kits with 1 ng or 100 ng of microbial genomic DNA followed by sequencing on Illumina MiSeq. Libraries prepared using PCR-free workflow of sparQ DNA Frag & Library Prep Kit with 100 ng of microbial genomic DNA shows similar performance as a typical amplified library prepared by Covaris mechanical shearing method.


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  • Maintains even coverage across a broad GC-spectrum and a wide range of input level
  • Low amplification bias results in PCR-free like coverage uniformity


High quality sequencing metrics

High quality sequencing metrics


High quality sequencing metrics

sparQ DNA Frag & Library Prep Kit generates high quality DNA libraries with minimal duplication artifacts. Libraries were prepared with 1 ng and 100 ng of microbial genomic DNA, amplified for 12 and 6 cycles respectively, and subsequently sequenced on Illumina MiSeq. Each library was down-sampled to 2 million reads (150 bp paired-end reads) and aligned to a reference genome with only unique alignments reported.


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  • High mapping percentage and low duplication artifacts
  • Industry leading sequencing results ensures better return on investment


NGS Automation

Quantabio sparQ Frag & Library Prep Kit can be fully automated

Currently sparQ Frag & Library Prep Kit is supported by the following vendors:

Looking for more information or for different automation vendor?

Contact Us

Vendor Automation Platform(s)
PerkinElmer Applied Genomics SCICLONE G3 NGSx
Tecan DreamPrep NGS
Beckman Coulter in development


sparQ UDI Adapter Resources

Setting up sparQ Library Prep kits in Illumina Experiment Manager

Technical Note - Setting up sparQ Library Prep Kit in Illumina Experiment Manager

Illumina Experiment Manager version 1.8 files (zip-download)

Illumina Experiment Manager version 1.9 files (zip-download)

sparQ UDI Adapter sequence overview

Performance Data

Fragmentation time course


Fragmentation time course

sparQ DNA Frag & Library Prep Kit is tunable to the desired fragment size. 100 ng Human gDNA was subjected to fragmentation with a series of incubation time points (3 – 18 min). After fragmentation, DNA samples were purified and then visualized using Agilent High Sensitivity DNA Kit.


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Streamlined workflow


Streamlined workflow

The streamlined workflow utilizes a proprietary enzyme mix that integrates tunable and reproducible fragmentation with DNA polishing simplifying library construction. The same single reaction tube is used to proceed to adapter ligation and cleanup, minimizing sample transfer steps. A second tube is used
for workflows requiring PCR amplification, and a final tube receives the sequencing-ready library.


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Fragmentation tuning guide


Fragmentation tuning guide

Simply select the desired fragment size and input DNA amount. If input DNA falls between values displayed on the graph, an estimate can be used for optimizing fragmentation times.


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Superior quality libraries & yields


Yield comparison

sparQ DNA Frag & Library Prep Kit shows significantly higher NGS library preparation efficiency. Libraries with 300 bp average DNA fragments from 100 ng of gDNA Coriell NA12878 were prepared using sparQ DNA Frag & Library Prep Kit and a commercial kit. Manufactures’ manuals were carefully followed. Amplified libraries (5 cycles of amplification) were quantified by Qubit fluorometric quantitation method


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Genome coverage analysis


Genome coverage analysis

Library prepared using sparQ DNA Frag & Library Prep Kit resulted in uniform coverage across the wide range of GC-content. Libraries were prepared using different DNA fragmentation and library preparation kits with 1 ng or 100 ng of microbial gDNA followed by sequencing on Illumina MiSeq. 2 million reads from each tested library were down-sampled and analyzed. Coverage uniformity against GC-content bias resulting from different DNA fragmentation and library preparation kits were compared by plotting normalized coverage for a wide GC-content.

Libraries prepared using PCR-free workflow of sparQ DNA Frag & Library Prep Kit with 50 ng of microbial genomic DNA shows similar high performance as a typical amplified library prepared by Covaris mechanical shearing method.


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Quality Sequencing metrics and improved workflow economics


Quality Sequencing metrics and improved workflow economics

sparQ DNA Frag & Library Prep Kit generates high quality DNA libraries with minimal duplication artifacts. Libraries were prepared with 1 ng and 100 ng of microbial genomic DNA, amplified for 12 and 6 cycles respectively, and subsequently sequenced on Illumina MiSeq. Each library was down-sampled to 2 million reads (150 bp paired-end reads) and aligned to a reference genome with only unique alignments reported.


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sparQ UDI Adapter Resource

For help setting up UDI’s in Illumina Experiment Manager Download

sparQ NGS Library Prep Solutions









What Customers Say
I have built >100 libraries with this kit and the results are great.
Genomics Core Director/Manager
West Virginia University
What Customers Say
The sparQ kit safeguards samples from over fragmentation and routinely provides more consistent fragment size. Once optimized, I had peace of mind knowing my... Read More The sparQ kit safeguards samples from over fragmentation and routinely provides more consistent fragment size. Once optimized, I had peace of mind knowing my samples were safe when I got busy in the lab.
Scientist, Laboratory Manager
Agricultural genomics institute

Details

  • Contents

    sparQ DNA Frag & Library Prep Kit contains:

    • DNA Frag & Polishing Enzyme Mix (5X)
    • DNA Frag & Polishing Buffer (10X)
    • DNA Frag Enhancer Solution
    • DNA Ligase
    • DNA Rapid Ligation Buffer
    • HiFi PCR Master Mix (2X)
    • Primer Mix
  • Storage & Handling
    Store kit components in a constant temperature freezer at -25°C to -15°C upon receipt. For lot specific expiry date, refer to package label, Certificate of Analysis or Product Specification Form.
  • Related Resources
    Product Flyers
    Product Manuals
    Technical Notes
    Publications
    Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase
    Jessica M. Nelson, Genome Biology and Evolution - 2019
    Abstract
    Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant–microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.
    Microbial mitigation of greenhouse gas emissions from boreal lakes
    Gaëtan Martin, Scientific Data - 2021
    Abstract
    The climate change crisis has drawn the attention of both the public and scientific community to the carbon cycle and particularly to the importance of greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4). CO2 has been a key component of Earth´s climate regulation throughout its geological history and is now the main driver of the current change in climate. CH4 has been responsible for a quarter of the cumulative radiative forcing observed so far. Recent studies suggest that lakes could be a major source of both CO2 and CH4. Boreal lakes are of special interest as they represent 27% of the global lake area, and their production of CO2 and CH4 are expected to increase in the future. This project aimed to investigate microbial processes with the potential to limit the emissions of GHGs from boreal lakes. For that purpose, the impact of an increase in phosphorus (P) concentration in the water on CH4 oxidation under the ice was investigated as well as the community composition of the methanotrophic guild. We also looked at the potential importance of chemolithoautotrophic microorganisms in fixing CO2 in the water column. Using a combination of geochemical analysis, genomic studies, and in vivo assays, we showed that P amendment has the potential to increase methane oxidation, possibly limiting the expected increase in CH4 emissions due to anthropogenic fertilization of boreal lakes. We also showed that methanotrophic community structure in boreal lakes is driven by CH4 concentration and that alphaproteobacterial methanotrophs might play an important role in removing CH4 from surface waters. Finally, we showed that dark carbon fixation is a common trait in boreal lakes and that it seems related to the iron cycle.
    ISSRseq: an extensible, low-cost, and efficient method for reduced representation sequencing
    Brandon T. Sinn, bioRxiv - 2020
    Abstract
    1. The capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of biology, including crop breeding, pathology, forensics, forestry, ecology, evolution, and conservation. However, access to the expensive equipment and bioinformatics infrastructure required for genome-scale sequencing is still a limiting factor in the developing world and for institutions with limited resources. 2. Here we present ISSRseq, a PCR-based method for reduced representation of genomic variation using simple sequence repeats as priming sites to sequence inter-simple sequence repeat (ISSR) regions. Briefly, ISSR regions are amplified with single primers, pooled, and used to construct sequencing libraries with a low-cost, efficient commercial kit, and sequenced on the Illumina platform. We also present a flexible bioinformatic pipeline that assembles ISSR loci, calls and hard filters variants, outputs data matrices in common formats, and conducts population analyses using R. 3. Using three angiosperm species as case studies, we demonstrate that ISSRseq is highly repeatable, necessitates only simple wet-lab skills and commonplace instrumentation, is flexible in terms of the number of single primers used, is low-cost, and can generate genomic-scale variant discovery on par with existing RRS methods that require high sample integrity and concentration. 4. ISSRseq represents a straightforward approach to SNP genotyping in any organism, and we predict that this method will be particularly useful for those studying population genomics and phylogeography of non-model organisms. Furthermore, the ease of ISSRseq relative to other RRS methods should prove useful for those conducting research in undergraduate and graduate environments, and more broadly by those lacking access to expensive instrumentation or expertise in bioinformatics.
    Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds
    Moritz Buck, bioRxiv - 2020
    Abstract
    Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.
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  • Testimonials

    The sparQ kit safeguards samples from over fragmentation and routinely provides more consistent fragment size. Once optimized, I had peace of mind knowing my samples were safe when I got busy in the lab.”

    Scientist, Laboratory Manager

    Agricultural Genomics Institute

    "I have built >100 libraries with this kit and the results are great."

    Genomics Core Director/Manager

    West Virginia University

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